An American family (consisting of father Ben Matheson, children Charlie and Danny, who is asthmatic, and Ben's girlfriend Maggie, a doctor) struggles in a rural farming village in a world that has been devoid of electricity for fifteen years. Ben's wife and the children's mother, Rachel, disappeared years before while hunting and is believed by all to be dead. Unexpectedly, troops from the Monroe Militia commanded by Captain Tom Neville arrive while Charlie is out hunting, intending to take Ben Matheson prisoner, because General Monroe believes that Ben may know something about restoring the power. Before Ben is arrested, he secretly gives Aaron a mysterious pendant with directions to meet someone and instructions to keep it safe. However, a militia soldier fatally shoots Ben, who was protecting Danny. The soldiers take Danny prisoner and leave. Ben requests that Charlie go to Chicago and find Ben's brother Miles, whom Charlie has never heard of, to help rescue Danny. Aaron and Maggie accompany Charlie. Along the way they meet Nate, who helps them out of trouble. Upon reaching Chicago they find that The Grand has been converted to a tavern owned by Miles -- and Miles immediately identifies Nate as a soldier in the Monroe Militia. After the militia unsuccessfully tries to arrest Miles, who slaughters the troops trying to capture him with Charlie's help, the group sets off to find Danny. Meanwhile, Danny escapes and meets a woman named Grace, but the militia come to her house and recapture Danny. Grace is then shown using another pendant to power a computer and communicate with an unknown party.

Charlie, Miles, Aaron, and Maggie continue to travel together looking for a way to find Danny. Miles insists that the group also needs his friend Nora, who they find has been captured by the militia. Charlie discovers Nate following her, captures him, and leaves him chained to a pole. As Charlie and Miles go to rescue Nora, Aaron shows Maggie the locket that Ben gave him. Danny continues his journey with the militia and is forced to watch as they execute a man for owning a gun and an American flag. Monroe tortures a member of a rebel group that are trying to bring back the United States. Nora escapes with Miles and Charlie and they find out that she had deliberately allowed herself to be captured to steal a sniper rifle that the militia had. They return to take the rifle and rescue the slaves she was held with, forcing Charlie to make her first kill. Nora tells Miles, much to his displeasure, that she has joined the resistance, who are trying to restore the United States. Meanwhile, a man stealthily shows up at Grace's house wearing a necklace just like hers, and Grace sends a frantic online message as she saw him that "Randall" was there. At the end, it is revealed that Gen. Monroe has been holding an uncooperative Rachel prisoner for years.

Now fleeing from the Monroe Militia, Nora leads the gang back to camp, only to find many of the fighters are injured from an earlier trap set by the militia. Besieged, they try to dig a tunnel to escape, while the sniper rifle Nora stole keeps the militia at bay, but the tunnel finally collapses. They capture the militia's commander, Jeremy, to use as leverage, but Jeremy tells the rebels that his troops are under orders not to deal for him because of Miles' presence, and then, realizing that the others didn't know Miles' history, tells them that Miles was the founder and former commanding general of the Monroe Militia. Miles gives himself up to Jeremy in exchange for the militia allowing Charlie, Nora and the others to get away, but Charlie and Nora later ambush the Militia on a bridge to rescue Miles. Meanwhile, Aaron and Maggie go in search of the address that Ben gave Aaron, which turns out to be Grace's, but find her house empty. Aaron finds it strange that she still had a computer, but he can't make it work. Later, the pendant powers up unexpectedly, making Grace's CD player and Maggie's iPhone work for a moment, but then everything goes dark again. Finally, Danny gets physically abused by a soldier bent on revenge, but manages to even things out.

Charlie and Nora meet back up with Aaron and Maggie. Unknown to them, Nate has escaped and continues to track Miles and Charlie. After running into a group of what appears to be stray dogs, Aaron is injured and Maggie is forced to kill one of the dogs. Miles sees and fights Nate and the group capture him. It is discovered that the dogs are the companions of a man who attacks the group and stabs Maggie in revenge for her killing one of his dogs. The group tries to save her, and Charlie is captured by the man. Miles frees Nate, and he and Miles kills the man and then went to find Charlie. Charlie has been tied to a chair with an elaborate, crossbow booby trap that will go off if the door to the room is opened. She escapes just as Nate and Miles enter the room. They return to Aaron, Maggie and Nora just as Maggie dies. Danny continues his journey with the Militia and they are forced to take shelter during a storm. Danny escapes and is quickly recaptured by Captain Neville. While taking shelter in a storm cellar, the roof falls in trapping Neville. Danny rescues him only to be put back into cuffs. Rachel continues to be a captive of the Militia and it appears she is being tortured for information on the blackout and Ben's involvement. Monroe taunts her with the knowledge that her son will arrive shortly.

After catching up with Captain Neville and the Militia at Noblesville, Indiana the group discovers a working steam train being prepared to take Danny to Monroe at the Capital of the Monroe Republic in Philadelphia. Charlie and Miles set off in town to look for Danny and Charlie runs into Neville. Miles and Neville fight and Miles escapes. They return and discover Nora has gone to find the local resistance member and plans on blowing up the train. They are about to question "Nate" when he escapes and returns to Neville who moves Danny to the train and brings his departure forward and plans on leaving right away. Nora plants her bomb in a log and plans on it being set off in the furnace of the train but after seeing Danny on the train, has second thoughts and is then stabbed by a member of the resistance who wants revenge on the Militia for his wife. Nora is found by Charlie and Miles and they chase after the train and Miles manages to get rid of the bomb before it explodes. Charlie finds Danny and Neville on the train and they fight. Nate joins the fight and captures Charlie but helps her and Miles to escape. The train arrives where Monroe has been discussing border skirmishes with the Georgia Federation and Plains Nation. When he shows Rachel that Danny has arrived, she explains she was also part of the project that Ben was working on and she draws a picture of the Pendant, explaining that twelve of them exist and that they are the key to getting the power back on. It is revealed that "Nate" is in fact Tom Neville's son, Jason.

Nora's condition worsens on the journey to Philadelphia; the party must find antibiotics in order to save her life. They are forced to turn to a drug kingpin named Drexel, who provides medical treatment, but not without a price. In return for the medicine, Charlie is tasked to assassinate the head of a neighboring family who has burned down Drexel's fields. Miles escapes from Drexel's compound to rescue Charlie and stops her just before she completes the task. Drexel is furious and makes Nora and Aaron fight each other to the death, but Aaron comes up with a ruse which leaves Drexel dead instead. Miles, Nora, Charlie and Aaron reunite and continue on the trek to Philadelphia.

Rachel and her son reunite and more information is dragged out of Rachel and her old "friends" before the black out. Charlie and the gang run into a group of self-governing children whose parents were killed by the militia about eight years ago. Miles feels responsible so he and Charlie devise a plan to get their leader, Peter, who was captured by the militia and sent to a militia ship. Though they want to do it alone, some of the children follow them, including Peter's brother Michael. Charlie lets the militia capture her and becomes a conscript. She escapes with Peter, but she is branded with the Monroe Militia symbol on her wrist. Miles and Nora also come to her aid, but Michael sneaks in, is captured, and used against them. Back at the lighthouse, where Aaron and the children are staying, Aaron's pendant randomly starts working, lighting up the lighthouse whose light distracts the crew of the ship while Charlie, Nora, and Miles kill the crew and free everyone. Back in Philadelphia, one of Rachel's old coworkers, Dr. Bradley, is captured because of his knowledge of the blackout thanks to the information Rachel provided. His daughter is hurt and captured, to force him to reveal all he knows about the blackout, including the location of his pendant. Miles asks Aaron for an explanation about the lighthouse and he is forced to reveal the existence and power of the pendant to Miles and Charlie. Meanwhile, it is revealed that Grace is being held captive by Randall.

When Nora encounters her sister, she must make a difficult choice between family and her promise to Charlie and Miles. However, when she learns that her sister is actually a bounty hunter and has made a secret deal with the militia to deliver Miles to them, she rejoins Miles' band to help them escape the ambush. Meanwhile, one of the most ruthless members of the militia, Strausser, is tracking Miles, Charlie and the gang. General Monroe hands Major Neville a stern warning. The locations of numerous pendants are revealed on a working computer screen in the unknown location where Randall is holding Grace prisoner.

Charlie and the group get closer to rescuing Danny. With the aid of the rebels they use abandoned subway tunnels to get under the walls of a heavily defended Philadelphia. However, their efforts are impeded when they begin to hallucinate due to oxygen deprivation after a subway tunnel collapses. During his hallucinations it is revealed that not only did Miles attempt to assassinate Monroe, but also that Miles fears that if Monroe asked him to rejoin the Militia, he would abandon his friends and do so. When they found the way out, one of the rebel members kills all the rebels and reveals that he's a spy working for the Militia. While holding Miles hostage, Charlie kills a Militia spy. After killing him, Miles, Aaron, Nora, and Charlie walks out of the tunnel to Philadelphia. Meanwhile, Rachel, still under duress by Monroe, purports to be building a device to enhance the radius of the pendant devices, but Rachel's former colleague Dr. Jaffe reveals it to be a bomb. In order to maintain her usefulness to Monroe, Rachel kills Jaffe.

Flashbacks: Unlike other episodes there are none for this episode. Instead the characters hallucinate.

Aaron, Nora, and Charlie are captured while hiding at the home of a friend of Miles after the four infiltrate Philadelphia. Miles takes Neville's wife Julia hostage and exchanges her for their safe return. Neville returns Aaron and Nora, and directs Miles to a defunct power plant where Charlie and Danny have been taken. Charlie reunites with her mother, Rachel, and her brother, Danny, at the plant. Rachel successfully completes the pendant amplifier before killing Strausser when he attempts to assault her. As Miles and Nora rescue Danny and Charlie, Miles faces off with Monroe to give the others time to escape. Monroe forgives Miles' treachery and pleads with him to come back and join his side, just as in Miles' hallucination. However, Miles refuses and fights with Monroe, and Miles then makes a quick exit when Monroe's soldiers appear. All of them escape after Aaron blasts a hole in the exterior wall with Nora's pipe bombs, but stop in their tracks when they hear a thundering sound and see a militia helicopter take flight using Rachel's amplifier and spool its minigun.

Miles' and Charlie's group flee from a newly functional Militia helicopter by hiding in an abandoned diner. The diner is destroyed by rocket fire from the helicopter, but the group survived in the reinforced walk-in refrigerator. After a short discussion, the group decides to warn and aid the rebels in their fight against Monroe's forces. Rachel and Miles are in need of anti-air weaponry, so they seek out another scientist, John Sanborn (Leland Orser), who is in possession of both weapons and another pendant. While alone, Miles tells Rachel that he saw her dead body and would never have abandoned her had he known she was alive. Sanborn informs Rachel that Randall captured Grace and then incapacitates them before revealing that he also is working for Randall. Miles, however, frees himself, incapacitates John, and takes the weapons and the pendant along with Rachel. Charlie and the others go to the rebel headquarters to warn the rebels, but the mood is grim as Commander Ramsey, the rebel leader, believes they can no longer win, but Nora says that Miles will help. Neville and his son Jason (formerly known as Nate) overlook a massacred rebel camp, while Jason voices his disapproval of Monroe's methods, because the rebels don't stand a chance. They eventually find the rebel headquarters and spot Charlie among many people there. Jason refuses to order an air strike, and he and Neville come to blows, with Neville beating him up and telling him to never come home. Neville then orders the air strike and tells Monroe that Jason is dead. Jason proceeds to warn Charlie, who is grateful but says he can't come with her. Monroe's helicopters arrive and the rebels take many casualties before Miles and Rachel arrive with surface-to-air rocket launchers. Miles aims his rocket launcher but is knocked out by the concussion from a missile. Danny then takes the rocket launcher and fires at the helicopter containing the amplifier, the source of power for both Militia helicopters. As the helicopters fall, Danny is killed by stray bullets to his chest. Later, Rachel cuts into Danny's body and pulls out a device with a flashing LED. Earlier, Grace is revealed to be working under duress for Randall to get the elevators working so Randall could go to Level 12 of the unknown location. Later, Randall Flynn and John Sanborn arrive in Philadelphia by car that works via pendant and offer their help to the Monroe Militia.

After Danny's sacrifice, Miles and Nora decide to go in search of his old top officers, the ones who supported his assassination attempt on Monroe, starting by Jim Hudson. He tells the rebels that Jim could help train them into real soldiers. Meanwhile, Rachel, Charlie and Aaron go to the rebels' Eco base, an old hospital. Things between Rachel and Charlie are strained, since Charlie is cold to her mother. Randall reveals that he can activate the pendants remotely to track them, and he and Monroe seal an uneasy alliance. After Rachel sees the pendants activate on their own, she realizes that Randall is tracking them, and she destroys the pendants so they cannot be tracked or used. Someone sees Miles and Nora and sells the information to a militia kill squad. Miles and Nora find Jim living under an assumed name as a happily-married town librarian. He's not happy to see Miles again and he refuses to go back. With Eco base under attack by Randall and militia troops, Rachel reveals that Randall was her boss at the United States Department of Defense (DOD), while Randall tells her through a megaphone that he needs her for her scientific knowledge. The militia kill squad arrives in Jim's town, but Miles, Jim and Nora manage to kill them. Randall captures Rachel and reveals to her that his intention is to restore power, but only in the hands of a chosen few, to prevent a return to the wars of the past. Charlie rescues Rachel. The militia's captain tries to kill Jim's wife. He saves her, but she's shocked by his background and repudiates him. Jim tells Miles he has destroyed his life again, but agrees to go with him. They arrive at the rebel camp in time to see Charlie apologize to her mother, and the two hug. Aaron asks Rachel for the truth and she agrees to tell him everything, starting with a place called "The Tower".

Paranoia strikes Monroe deeply as Neville disappears and word reaches him that Jason is with the rebels. Miles, Charlie and Nora infiltrate the Georgia Federation to chase the nuclear device, which Monroe has had Miles' former protege Alec plant in Atlanta, the federation's capital. During a battle, Alec tells Charlie to ask Miles what he did to Rachel. Monroe uses a helicopter to drop leaflets over Atlanta demanding unconditional surrender. Miles is captured by Georgia police and turns out to have had a personal relationship with Georgia Federation president Kelly Foster, who ultimately frees him to find Alec. Miles kills Alec just as Monroe orders Alec to detonate the nuke. Meanwhile, Rachel and Aaron locate her former co-worker Dr. Jane Warren (Kate Burton), who reveals that the nanites kept Danny and keep her partner Beth alive through their cancer-eating abilities. Jane believes that if Rachel shuts down the nanites and restore the power, Beth will die. However, at Beth's urging, she provides Rachel with her technical journal, which has information that will permit Rachel to turn off the nanites if she reaches the Tower. After the nuclear weapon has been disarmed, Charlie asks Miles about Rachel, and Miles answers only that he hurts anyone close to him. President Foster declares war on the Monroe Republic and offers Miles command of an army made up of 200 soldiers from the Georgia Federation, to help the rebels open a second front within the Monroe Republic.

Miles is now in command of the combined rebel forces and 200 Georgian troops. His capture of three southern outposts of the Monroe Republic draws the attention of Monroe, who reminds Jeremy that the militia started with a few small victories. Monroe, Jeremy, and several troops travel by helicopter to Miles' and Monroe's home town and round up all the citizens, including Emma (Annie Wersching), Miles' former fiancée and Bass Monroe's former lover, and Monroe sends a runner to Miles stating that he will execute everyone if Miles does not come alone and surrender. Although Miles sneaks away from camp at night, he is later followed by Charlie, Nora, Jim Hudson and some Georgian soldiers. In the battle that ensues, Emma tells Bass that she gave birth to his son while he and Miles were away in boot camp, but she is then killed by a Georgian officer trying to shoot Monroe. Miles shoots and kills the Georgian officer for killing Emma. Jeremy leads a wounded Monroe back to the helicopters. Meanwhile. Aaron and Rachel cross the Mississippi River into the Plains Nation on their way to The Tower. The pair stop in La Grange, Missouri , where Rachel tries to decipher the diagrams in Jane's journal. She declines help from Aaron, who has two technical doctorates from MIT, and asks him instead to shop for supplies. While doing so, Aaron sees his wife, Priscilla whom he abandoned in the months right after the black-out, but she acts cold and distant. Priscilla tells Aaron that she has moved on, but Aaron believes her actions indicated that she was in trouble. He ultimately finds that she was being held by a bounty hunter and rescues her (with her help). She tells him that she has remarried and her family is in Texas; the Monroe Republic put a bounty on her after she killed an official while defending her eleven-year-old daughter. They say goodbye. President Foster decides to appoint a former militia officer who has defected to her side as her new liaison to Miles: Tom Neville.

The Rebel and Georgia Federation Alliance is attacked by the Monroe Republic, reducing their numbers from 300 men to 30. This prompts President Foster (Leslie Hope) to tell Miles that either he comes up with a plan, or she will surrender to Monroe in order to save her people. During the attack on the Rebel/Georgia Alliance, Jason is critically injured, but is carried to safety by his father, Major Neville. Monroe kills Jeremy Baker (Mark Pellegrino) believing him to behind an assassination attempt made against him. It is later revealed that Baker had nothing to do with this assassination attempt, strengthening Baker's statement that he made before he was killed, pointing out that the only reason all of Monroe's friends betray him (including Major Neville and Miles) is because his delusions, paranoia, and barbaric nature drive them away. Rachel has Aaron reprogram the flashing LED, which she explains to be first-generation nanotechnology, that she had removed from Danny after his death, and inserted it into her leg to repair the bone and tissues. When Rachel's leg is healed, a group from the settlement saw how her leg was healed and force them to heal one of the group's son, who has been injured and has infection in his wounds. They agree to help the boy, but when they arrive at the electronics store where Rachel's leg was healed, Rachel knocks the boy's father out. Rachel then says that she has to go the Tower first because she has to restore the world's electricity so that the opposing nations could overthrow Monroe and end his ongoing war. She also reveals that she wants revenge on Monroe for killing her son, and ruining her life. At the end of the episode, Jason and Charlie are witnessed by Tom, kissing in a hospital room within the Georgia Federation Presidential House. Nora is captured by the Monroe forces and delivered to Monroe, where it is revealed that they knew each other previously.

Rachel unpins the grenade in Monroe's tent, but one of Monroe's bodyguards pushes her out of the way. Another militia soldier tackles Rachel and throws the grenade outside just in time. Aaron witnesses Rachel being led in chains, eliminating his chance to get into the Tower. Rachel is allowed access into the Tower, much to the astonishment of Randall. The group inside the Tower witnesses Monroe's entry as the leader, named Dan Jenkins, orders his men to take their weapons to fight Monroe. ( Dan Jenkins is the same man who was the Tower's commander and who took Randall's order to activate the machine that caused the blackout). Miles lands the helicopter four miles from the Tower On his groups hike to the entrance of the Tower, they run into Aaron. Aaron tells Miles that there is a way into the Tower, but they have to find a way around Monroe's troops. Inside the Tower, Randall shows Monroe the control room, where the U.S. government's satellites still have live feeds of the entire planet. According to Randall, the Tower has the capacity to do anything and is impervious to everything, including the Blackout. However, they first need to go to Level 12. Rachel is shocked when Randall reveals this, but Monroe and his troops enter the elevator, ready to witness the entirety of the Tower's potential. Monroe and his group take the elevator to Level 12, but it stops at Level 11. Monroe's men step out of the elevator, but an alarm sounds and Jenkin's men, using superior coil gun weaponry, begin to take down Monroe's men. Rachel runs for cover in a room that was a vice-presidential bunker, but Monroe follows and pins her, demanding to know who the attackers are. Outside, Tom Neville and Jason take out the Militia encampment's power source with grenades. Aaron and Miles rush to open the doors of the Tower as Monroe's men descend on them. However, only Miles, Charlie, Nora, and Aaron can get in, leaving Jason and Neville outside when the door shuts. The Militia captures Jason and Neville, but they manage to plot a revolt with the assistance of the local commanders they meet during interrogation. At the Tower, Rachel tells Monroe that he killed her son and her son's death was his fault, but Monroe tells her that he doesn't know how he got out of control and reveals to Rachel that he also has a son, too. Meanwhile, Miles, Charlie, Nora, and Aaron are in the battle with the attackers. Monroe decided to help Rachel save Charlie, but he has to kill Miles. During the fight, Miles and Nora are separated from Charlie and Aaron, and Monroe separated from Rachel, with Miles face to face with Monroe. Rachel, Charlie, and Aaron are captured by the attackers and are led to a place where there are families. They grow their own food and live to protect the Tower, especially Level 12. Rachel realizes that the inhabitants at the Tower are the workers and scientists. Grace Beaumont and Dan Jenkins burn Doctor Warren's journal in order to prevent Rachel and Aaron from turning the lights back on. This is because there are two possible results of deactivating the nanites. It could turn the lights back on, or it could set the world on fire.

Flashbacks: One week before the Blackout: we see Ben working on something for Randall. Ben and Rachel are having disagreements due to the stress of the project. Rachel wants to spend time apart after the project is launched.

During the fight between Monroe and Miles, they are attacked by the Tower's inhabitants, and Miles is separated from Nora when he and Monroe are flown away out of the Tower. After waking up outside of the Tower, Miles fights Monroe and beats him. When Miles is about to leave him, Monroe reveals to Miles that everything he has ever done has been for Miles, as he has always followed him to have his back. In addition, he states that the war between him and Miles began when Miles attempted to kill him. Miles reveals that he could never kill Monroe as he still considers him his brother. After that, Monroe is captured by his own men. Meanwhile, Aaron discovers that his code from MIT was sold to the Department of Defense, and was used for the Tower's operating system, much to his shock. Later, Miles rescues Monroe from the new Monroe Republic, headed by Tom Neville, who led a revolt against Monroe. Miles tells Monroe to run, while he enters the Tower. Meanwhile, Charlie, Rachel, and Aaron escape their way to Level 12, and later reunited with Nora. Nora is shot in the abdomen while creating a way for Rachel, Charlie, and Aaron to reach Level 12, Charlie stays with Nora while Rachel and Aaron makes their way to Level 12. Miles is reunited with Charlie and Nora, who later bled to death and subsequently dying in Miles' arms. While heading down to Level 12, Aaron and Rachel are confronted by Neville and his Militia, who entered the Tower, first. It is later revealed that Neville decided to become the leader of the Monroe Republic, himself. Neville orders them to surrender, but Miles and Charlie helps them escape. After arriving at Level 12 Aaron runs the shutdown command for the nanites, re-instating electric power worldwide. As the power is re-instated, President Foster of the Georgia Federation orders military strikes on Philadelphia, and lightning begins to strike the surface of the Earth at a rapid rate. However, the victory is short-lived as Randall appears and reveals he has been attempting to gain access to Level 12 for a long time, not to turn the power back on for everybody, but for the purpose of sending out ICBMs aimed at Atlanta and Philadelphia in order to reunite the states into one entity, quoting Lincoln's famous line, "A house divided against itself cannot stand." Randall then proceeds to say that everything he did was so "this great nation shall not perish." When Rachel asks him why he is doing this, Randall smiles, calls himself a Patriot, and then shoots himself in the head. At the end, the camera shows a room with an American flag, where someone is turning a lamp on and off. Another person enters the room saying that Flynn has succeeded in his mission, and that, "It's time to go home, Mr. President." The camera zooms out and the location is a U.S. Colony at Guantánamo Bay, where the President of the United States has presumably been hiding for the past 15 years, waiting for Flynn to fulfill his mission.

Set six months after the events of Season 1, the episode is broken into three storylines. Miles, Aaron, and Rachel have settled into life in the Texas town of Willoughby. Rachel was brought to the town in emotional shock after the events of the Tower. As hoped, her father, Gene Porter, is still alive and living in the town, and is willing to help Rachel recover. It is confirmed that the nuclear missiles bound for Atlanta and Philadelphia struck their targets, creating widespread devastation and throwing both the Monroe Republic and the Georgia Federation into disarray. Meanwhile, in a refugee camp outside of Savannah, Georgia, Neville and Jason desperately search for Julia, Neville’s wife. They witness the return of the U.S. Government, and a group calling themselves "The Patriots". One of the Patriots, Secretary Justine Allenford, gives a speech about how the U.S. Government is back to help its people, but Neville becomes suspicious. He believes that the Patriots were behind the nuclear bombings on Atlanta and Philadelphia. Meanwhile, Charlie is hunting for Monroe in the Plains Nation, and comes upon him pit fighting in a small town. She tries to assassinate him but misses and witnesses Monroe abducted by two men. The episode concludes with an attack on Willoughby by a warrior clan from the Plains Nation. In the attack, Miles is captured and brought before the tribe’s leader, Titus Andover. Aaron is killed protecting his girlfriend, but unexpectedly opens his eyes in the final moments of the episode.

Aaron wakes up after being dead for hours. Rachel and Gene discover that he's alive, much to their shock. Aaron begins to believe that the nanites were responsible for bringing him back to life. Meanwhile, Miles is held captive by Titus Andover and his tribe members. The holding area contains a red door through which prisoners are taken and do not return. The town discovers that the sheriff is dead and Miles is being held captive. Rachel tries to organize a rescue for Miles, but no one agrees to join her, eventually leading her to try to rescue him on her own. While Rachel is leaving town, Gene and the others join her. Miles tries to escape, but gets caught instead. He is brought before Titus Andover who, after revealing his history, smashes Miles' right hand with a hammer. It is revealed later that a key member of Titus’ group is a Patriot. Back at Willoughby, Aaron reveals to his girlfriend Cynthia the truth behind the blackout and his resurrection. Meanwhile, Charlie is captured by Monroe’s abductors and discovers they are contracted by the Patriots. The lead, Adam, notes that the Patriots need Monroe alive. The pair let Charlie go and ride off with Monroe, only to have Monroe escape. Charlie manages to save Adam but not his partner. In Savannah, Neville organizes an assassination attempt on Allenford, but turns on the would-be assassin to further his goal of infiltrating the Patriots. At the tent, Allenford allows Neville to join the Patriots. The episode closes as Miles is brought behind the red door where Titus is next to a sick woman who is receiving a blood transfusion from a dead man lying on a table nearby.

In Willoughby, Texas, as Miles and Rachel discuss Ken's death, Aaron knocks on their door to confront Miles about the situation at the rail road. Aaron says he is pretty sure he caused the men to catch fire, and Rachel thinks it might be the nanotech. Shortly after, Monroe, Charlie and a contingent of Texas Rangers arrive in town. After pointing guns at each other, the Rangers and Patriots lower their weapons. However, the Patriots make efforts to hide their activities from the Rangers. Miles contacts the lead Ranger, Fry, whom he tried to kill when he was in the Monroe army, as he is their best shot at starting a war with the Patriots. Fry demands proof to take back, otherwise Texas will sign a treaty with the Patriots. Charlie and Monroe make contact with Miles and aid him in the capture of the Patriot soldier who was working with Titus. As they prepare to question him at a hidden location, Aaron and Rachel arrive due to a vision Aaron had of the location. As they hide and the Ranger arrives, Miles discovers the soldier committed suicide with a cyanide tooth. Monroe kills Fry in order to frame the Patriots as a way to start the war. In the Savannah Refugee Camp, a wagon is mobbed by desperate people who want to board. Neville speaks with Allenford, who tells him she is being called to D.C. and he is to accompany her as her security force. Along the way, they are ambushed by Patriots, who try to assassinate Allenford. Neville and Allenford escape, although Allenford is wounded. When they stop to rest, Allenford reveals that the wagon was actually taking people to reprogramming centers, the same one where Neville's son is now. She tells Neville that the Patriots are brainwashing innocent people to become members. She also knows that the Patriots were sent to kill her, in order to silence her for objecting to them. After Neville begins to leave her to die from her wounds, she bargains to take him there if he helps her.

Miles and Monroe set about making the ranger look like he was killed by the Patriots, sinking his body in the river. The Texas Rangers follow Fry's tracks to the old warehouse and find a gun casing from a Patriot gun. Miles catches Monroe with a Patriot body and Monroe gives him information that the Patriot disclosed before Monroe killed him. Monroe is sitting in a building when someone throws in a stun grenade. He leaves the building to find a number of Patriots with their guns pointed at him, and he is taken into custody. Instead of the intended war, the Texas Rangers and the Patriots are working together. They present Monroe to the public and say he will not live to see another sunrise if he is found guilty of his crimes at an immediate trial. Reporters and old flash cameras are there to capture the moment. Aaron meets Bonnie Webster (Alanna Ubach), who has entered the town with the Texas Rangers. Miles tells Charlie they have to get Monroe out. At night, Miles and Charlie sneak along the top of a building. They see Monroe being moved to a vault in the bank and Miles confronts Rachel about tipping off the Rangers and Patriots that there was going to be a jailbreak. Rachel confesses to telling them. Charlie and Rachel have a confrontation: Rachel tells her she cannot bear to lose another child, but Charlie says Monroe saved her life. In the courtroom, Monroe is sentenced to death. Monroe's last request is to see Miles. Monroe asks Miles to shake his hand and say goodbye and to find his son by Emma. Miles tells Monroe he hid his son from him, much to his shock. At midnight, Monroe is given the injection by Gene Porter and dies. Miles is broken by the loss of Monroe and tries to drink his pain away. Allenford tells Neville the direction of the camp his son is being held in, then refuses to go any farther. Neville tells her he is not letting her go until he lays eyes on his son. They find dead bodies ripped apart, and Allenford reveals it is the work of the Patriots' bootcamp. Soldiers fire on them and they run. The main attacker turns out to be Jason, who does not hesitate as he attempts to kill his father. Jason and his group storm through hallways of the warehouse and Jason's vision is blurry. Allenford says that Neville's son is no longer his son. She knows this because her own son has been put through this program in Cuba, and her husband is a high ranking Patriot who puts country before family. Neville kills the other two with Jason and holds Jason at gunpoint. Jason beats up Neville and is trying to killing him when Allenford hits him over the head, knocking him unconscious. Rachel stands over Monroe's grave and begins digging.

Monroe is dug out of his grave by Rachel, having been heavily drugged to make him appear dead. He rehabilitates in a farmhouse outside of town. Dr. Horn, science adviser to the Patriots, arrives, having been drawn by news of Rachel's presence and strange happenings that have occurred since her arrival. With the help of Gene, Dr. Horn learns that Aaron was the cause of the strange happenings, including the spontaneous combustion of two soldiers. Miles and company are aware of Dr. Horn's interest in Aaron and conspire to help him escape town. Aaron won't leave town without his girlfriend, who ultimately agrees to come with him. Gene agrees to help Aaron escape, but is coerced by the Patriots into setting up his capture. On a hunch, Miles observes Gene aiding the Patriots, which devastates Rachel. When Aaron fails to arrive at the rendezvous, the Patriots realize Gene's cover is blown. They lock down the town and aggressively search house to house. Aaron and company make for a sewer line that leads out of town and barely escape. At the end of the tunnel, they are confronted by Patriot soldiers, but are suddenly helped by Monroe. However, in the fighting, Aaron's girlfriend is attacked by a soldier, triggering another nanotech attack by Aaron. As they walk to safety with Monroe, Aaron's girlfriend is terrified of him. Meanwhile, somewhere on the east coast, Neville and Allenford are hiding out as Jason wakes up. The drugs are being flushed out of his system, but Allen still questions his trustworthiness. After getting ambushed by Patriot cadets, Jason seems to betray both Neville and Allenford, but instead kills their attackers and offers the knife he used to his father. Allenford wants to try to reclaim her son in Cincinnati after Jason helps, but she is unexpectedly drugged by Neville. She awakens in handcuffs, and is questioned by Neville about the location of her husband.

Miles and Rachel are interrogating a captured Patriot soldier when they are informed by Charlie about a statement Truman made to the town, claiming Miles and Aaron were behind the store bombing. Rachel tells Charlie that the Patriots will never stop looking for them unless they kill Horn. After realizing the Patriot HQ is in the town paper factory, they devise a plan to send Rachel to drop poisonous gas into the factory. Monroe, Aaron, and Cynthia are waiting for Miles to come for them. Cynthia asks Aaron if he killed Carl, her ex-husband, and he says he did but he can't control his powers. Aaron breaks down in tears and asks Cynthia to leave him alone. They are discovered by Patriot soldiers sent by Horn, who Monroe attempts to fight off. On the verge of being overwhelmed by too many Patriots, Monroe flees, leaving Aaron and Cynthia to be captured. Miles calls off the mission when Gene enters the factory, but Rachel continues anyway. As Rachel prepares to drop the poison, Aaron and Cynthia are led into the factory. Miles stops her just in time. Inside the factory, a drugged Aaron begs Horn to let Cynthia go. Cynthia realizes Gene is there and that he is collaborating with the Patriots. Horn refuses to let her go, saying she is assurance that Aaron will not torch the factory, and orders Gene to leave. As Cynthia sits in a cell, she hears Aaron screaming from being tortured by Horn. Horn observes Aaron’s skin healing when cut. Miles, Rachel, and Charlie kidnap Gene and question him. He says the Patriots were the ones who gave him the medicine way back when and he took it. Truman shows up demanding they all come out. Gene emerges, alone, and holds a knife to Truman's throat. The soldiers chase Miles, Rachel, and Charlie. Truman holds a gun to Gene's head and takes him back to the factory. Horn brings Cynthia into the room to see if Aaron can heal her when they cut her. Aaron screams as they stab her in the back and the fire flashes. Meanwhile, in North Carolina, Neville walks into a Patriot camp to see Commander Roger Allenford. When asked his business, Neville holds up a ring. He convinces Allenford that although the commander’s wife is alive, she is an enemy of the Patriots. Neville says if Allenford brings his own wife in for justice, it would raise his standing in the eyes of the Patriots. Neville further convinces the commander that bringing her in would ultimately protect Allenford’s son and the commander’s life. At the barn where Justine Allenford is being held captive, she asks Roger (her husband) to kill Neville and Jason and then run away with her, but Roger says there is no place to run to and shoots her.

Miles, Rachel, and Charlie move to rescue Aaron. They discover all the soldiers knocked out and Aaron and Cynthia gone. Following their escape route, they look in a fog-shrouded forest, with the Patriots searching too. They are eventually joined by Monroe and follow the trail to a local high school. At the high school, Aaron wakes up next to Cynthia, alive and apparently healed from her injuries. He discovers a small boy who says he lives there. After Cynthia wakes up, she notes that she does not see the boy and it becomes apparent that the boy is a manifestation of the nanotech. The nanotech says it has been helping Aaron because he woke it up. The Patriots arrive at the high school just before Miles and company. A competing search begins for Aaron. Miles collapses from his arm infection and confesses his love for Rachel as Patriots burst in. Neville boards a train bound for Washington D.C. with Jason and Commander Allenford. They are headed for the White House. His wife boards the train too, although she is newly married. After reuniting, they conspire to greater political ambitions. Horn discovers Aaron fleeing and holds him at gunpoint. After Horn shoots dead Cynthia, the boy reappears. In his grief, Aaron requests that the boy kill all the Patriots in the school. He complies, but wonders why Aaron did not ask for Cynthia to be healed. The boy is confused and vanishes, leaving Cynthia dead and Aaron alone.

Grace leaves Aaron and Priscilla in Spring City, Oklahoma. Aaron receives a visit from the nanotech taking the appearance of Cynthia, saying that he and Priscilla have to go to Lubbock, Texas. After arriving at Willoughby, Miles, Monroe, Rachel and Connor discover that a typhus outbreak has hit the town. Rachel decides to infiltrate the quarantine camp. Meanwhile, in the quarantine camp, Gene and Charlie are forced to work together with Truman and the Patriots in order to save the town. Rachel shows up to help the ill and to get more information about the disease. She finds out that the Patriots are poisoning people with problems (epilepsy, alcohol addiction) to make a pure race and are using the outbreak as a cover. She assumes that the Patriots have an antidote for the virus they created, and when Gene becomes sick she sends a note to Miles and Monroe to get it. Miles and Monroe are outside the camp, and they look for the antidote in a Patriots' warehouse. Not finding anything, they kidnap Truman, injecting him with infected blood to force him to reveal the location of the antidote. Connor accompanies Truman into his office where he can retrieve the antidote. However, he is surrounded by Patriot soldiers before he can leave, holding Truman at gunpoint. In Washington, Julia and Neville try to get information about the incarceration of their son Jason. Julia searches her new husband's office and finds out that he is in Kenilworth Prison. Julia and Neville try to capture her husband, Doyle, Chief of Staff, in order to force him to show them to their son. However, he learns of their plan and has them both arrested.

Miles and Rachel escape from Neville and Jason, who are working for the Patriots, and reunite with Monroe, Connor and Charlie, along with Duncan's men. They find out that the quarantine camp featured previously has been converted into a re-education camp, which was built by Doyle. They also find that the re-education camp is using children from Willoughby and other towns. One of the kid's fathers inadvertently activates programming in his daughter cadet when he recites the numbers from a tattoo discovered on her eyelid. They return to the encampment, only to be attacked by Neville and Truman. Before they escape, Rachel convinces Miles let the cadet go. In Washington D.C., President Jack Davis is told by Commander Allenford that the re-education centers are up and running. Meanwhile, Aaron continues his journey to Willoughby with Priscilla, who is later enveloped by nanotech fireflies.

Now outside of Austin with the Texas Rangers in pursuit, Miles leads them away to buy Monroe, Connor and Charlie time to escape and return to the camp. Knocked from his carriage and confronted by the rangers, Miles fails to reason with them and is seriously injured in the ensuing gunfight. With the rangers now dead, Miles makes his way to an abandoned house but ends up trapped in the basement, alone and wounded, where he attempts to treat his wound. Meanwhile, Charlie and Rachel decide to search for Miles along with Monroe. During the search, Charlie is confronted by Neville who demands to know where Jason is. She leads him to a house, but he holds her at gunpoint, forcing her to reveal that she had previously killed Jason in self defense. Meanwhile, Aaron continues to deal with the nanotech-controlled Priscilla's demands, and learns that she knew where Miles was, but believed him not worth the effort of saving. Desperate and alone, Miles successfully escapes from the basement after burning the ceiling.