Ida suffers under the strict thumb of Deaconess Matron Martha, while making friends with shy young nurse Therese. Therese is attracted to Ida, as is medical student Georg Tischendorf. While Ida's job at the clinic gets her interested in medicine, artistically talented Georg is just studying to please his father. Behring tells Ida that women can study medicine in Switzerland but not in the German Reich, and gives her books to read. Koch starts an affair with Hedwig, and is trying to keep this a secret. Liberal reformers in the Reich like Virchow hope for a political thaw now that Kaiser Friedrich III has ascended the throne. But Friedrich is diagnosed with laryngeal cancer. The treatment by the surgeons of the Charité cannot save him and he dies after a reign of a mere 99 days, leaving his nationalist son as the next Kaiser, Wilhelm II.

Dr. Ehrlich's wife Hedda is ready to give birth, but the midwife cannot get the fetus turned the right way. When the child's pulse starts to fade and the situation becomes critical, there is only one surgeon left at the clinic who can help: Emil Behring. Dr. Behring saves Hedda's life, but her child dies. Meanwhile, thousands of physicians from around the world arrive in Berlin for the World Medical Convention to hear Koch speak: his careful announcement of a possible remedy for tuberculosis causes excitement in the international medical community. But the drug has never been tested on humans.

Hagenbeck's "Peoples of the World Show" at the Berlin Zoo brings an unusual patient to the Charité: an Indian woman has come down with variola (smallpox), a disease which has been wiped out in Germany thanks to inoculation. Virchow, the unchallenged star at the Charité again after his triumph over his colleague Koch, is fascinated by anthropology and accepts the patient as an object of demonstration. Nursing assistant Stine keeps her distance, but she begins to feel affection for the Indian woman when she cares for her as she is dying. Koch becomes an outcast. Only his closest friends come to his wedding with Hedwig, including Ida and Dr. Ehrlich. Koch's scientific failure also unjustly discredits Ehrlich and Behring's work. No one at the Charité wants to try their diphtheria serum on human patients. This plunges Behring into a deep depression. Ida suspects that the brilliant but sensitive man needs a strong woman at his side – and thinks she is willing to give up on her dream of studying medicine for his sake. Georg has seemingly abandoned any idea of marrying her.

Anni Waldhausen, a pregnant medical student, takes her exams. Her professor is Ferdinand Sauerbruch, a surgeon who grew to fame at the Berlin Charité for inventing a surgical technique that prevents amputation of a patient's damaged thigh. Anni does not want to practice medicine before her child is born and focuses on writing a thesis about self-mutilation. Her mentor, Max de Crinis, is head of the psychiatry ward at the hospital and a Nazi official. Anni's husband Artur is chief resident of the children's ward. He is testing a new TB vaccine on disabled children in state custody. Anni's brother Otto has recently returned from his frontline duty to continue his study of medicine. He gets a job as a clinic clerk and makes friends with Martin, an orderly and former soldier with a leg prothesis who quickly realizes that Otto's easygoing personality is just an act to hide his severe PTSD.

Anni nearly dies due to severe blood loss, but is saved by Professor Stoeckel. Her daughter does not show any life signs, but is successfully revived by the doctors. Anni shares a room with Magda Goebbels who is suicidal because of a recent miscarriage. Artur tenderly cares for Anni while Goebbels' husband is nowhere to be seen. Magda Goebbels is constantly drunk, makes sarcastic remarks about life and admits to Anni that her marriage has become nothing more than a façade. In the meantime, Sauerbruch has a new colleague. Adolphe Jung is a surgeon from Strasbourg and has been transferred to Berlin. Together they save a young boy named Emil who is seriously hurt. Christel, a nurse and avid Nazi supporter, finds a leaflet of the White Rose that belongs to the patient. She wants to report Emil, but Martin tears the leaflet apart. She wants to report Martin, as well, but Otto swiftly asks Christel out on a date when she threatens to. Martin witnesses this and realizes that Otto rejects the regime, just like him. Christel tells Otto that Martin regularly has to report himself to the police. When Otto asks Martin about, Martin denies it.

Artur punctures Karin's head to decrease the pressure on her brain, a procedure which seems to work at first since her head develops normally. Sauerbruch is visited by Karl Bonhoeffer who was de Crinis' predecessor. Bonhoeffer tells him that Hans von Dohnanyi, his son-in-law, was arrested, had a stroke in prison and is now paralyzed from the waist down. He asks Sauerbruch to take him in and protect him, which Sauerbruch agrees to. De Crinis wonders whether von Dohanyi is just a malingerer and orders Nurse Christel to watch him at all times. Karin's brain pressure increases again. A desperate Anni and Artur plead with Sauerbruch to perform a potentially life-threatening surgery on their child. Sauerbruch operates on her secretly, but is overwhelmed by the complexity of the surgery. Jung saves Karin by successfully finishing the operation. Artur asks Sauerbruch to keep Karin in the surgical ward, since she wouldn't be safe in the children's ward because of his superior Professor Bessau who supports the euthanasia program. Otto is angered by his sister's naiveté and bluntly tells her that children like Karin are usually killed. Anni doesn't believe him, but realizes the truth when she looks at documents about her husband's experiments and discovers that all test subjects are disabled.

Karin can return home in January 1944 after her recovery. Käthe, a children's nurse, suspects the true reasons for her hospitalization, but Artur and Anni assert that she fell from her changing table. Artur tells Anni that he got new test subjects, but avoids the subject when she wants to know more about his experiments. De Crinis keeps trying to prove that von Dohnanyi is not really sick, but Sauerbruch urges him to wait before creating a profile, to which de Crinis grudgingly agrees. Both Dr. Jung and Margot Sauerbruch fear that Fritz Kolbe, the lover of Sauerbruch's secretary Maria Fritsch, is a Wehrmacht spy who gives clinic information to his superiors. When they catch him taking photographs of documents, he admits that he is actually a member of the resistance and provides the Allies with information. Dr. Jung and Margot offer their support. Margot takes the information and accompanies her husband to Switzerland where he wants to give a lecture and gives the information to a contact person. De Crinis exploits Sauerbruch's absence to declare von Dohanyi a malingerer and gets him arrested again. A woman who had been buried under debris gets admitted. She becomes apathetic when she learns that her missing son probably died. De Crinis says that she suffers from hysteria and orders Otto to prepare her for a euthanasia program. Otto tells Anni about this, but she doesn't seem to care and says that euthanasia programs were just made up by the Allies. A short time later she realizes that an admitted orphan is the woman's son and reunites them.

There are more and more air raids on Berlin. Because of this, a surgery bunker has been built in the Charité's yard which soon becomes crowded and is not well equipped. Von Stauffenberg has returned from his military service in North Africa and had his hand amputated. Sauerbruch wants to provide him with an innovative prosthesis called Sauerbruch-Arm. His injuries are also the subject of Otto's exam questions. He struggles at first, but ultimately passes his test. Karin's therapy is useless,which is why Artur sends her to the Kinderfachabteilung without Anni's knowledge. Anni discovers this and intervenes before Karin is transported. She secretly hides her in the attic of the bombed out staff apartments. Artur questions his wife when he learns that Karin never arrived at the clinic, but Anni does not tell him anything.

In early 1945, Sauerbruch and his staff have to operate on wounded soldiers and civilians with only a very limited amount of medicine, water and electricity available. Anni and Artur avoid each other; Artur wants to save their relationship nonetheless. He notices that an admitted boy with severe burn wounds who recently lost his mother and sister in a concentration camp is Jewish, but does not give him away. Later, the boy's father gives him a Yellow badge which will protect Artur from the approaching Red Army as they will think he is Jewish. Anni steals Artur's key to the hospital food stocks to take food for the hidden Karin and Otto, but Artur realizes and confronts her. Martin meets some underaged Volkssturm soldiers who are determined to defend the heavily damaged city from the incoming Soviets. They are led into the hospital by Christel despite it being declared a neutral zone. Martin tricks the group, locks them in the basement and tells them he will only release them if they throw their guns out the window. He ignores Christel's protests while telling her that the child soldiers have mothers who will thank him later. Karin is brought to the bunker while Otto stays in his hideout because deserters are still being executed even though the war is almost over. De Crinis is approached by Magda Goebbels, who asks him to give her potassium cyanide because she wants to kill herself and her children. De Crinis says he only has two pills, for himself and his wife, and recommend Frau Goebbels to give anesthetics to her children to avoid seeing their spasms; shortly afterwards De Crinis and his wife commit suicide upon being blocked by Red Army soldiers. The Soviet soldiers reach the bunker and hold the medical staff at gunpoint, but do not harm anyone once they know about Sauerbruch's medical abilities, and make him and his team tend to their wounded comrades. Christel is shot during one of the last shoot-outs in the streets while Otto gets hit by a stray bullet, but Martin saves him by getting him to the bunker. It is announced that Hitler has committed suicide, and Artur leaves the bunker to surrender to the Red Army, which evacuates the bunker.