In 1986, four weeks after the disappearance of Mads Nielsen, a desperate Mikkel is found by police chief Egon Tiedemann, who suspects he has been beaten by the teenage Ulrich. Mikkel is brought to the hospital by Ines, then a nurse, who gains his trust. At the nuclear plant, newly elected director Claudia Tiedemann, Egon's daughter and Regina's mother, clashes with her predecessor Bernd Doppler, who informs her of secret barrels hidden in the nearby caves. Bernd's son Helge, gives Claudia a book: Eine Reise durch die Zeit (A Journey Through Time) by H. G. Tannhaus. Meanwhile, as the town's electricity is flickering, a teenage Charlotte starts investigating the deaths of multiple birds, shy young Hannah has unrequited feelings for Ulrich, and Regina is being bullied and engages in self-harm. A flock of sheep is found dead from cardiac arrest with their eardrums ruptured, Mikkel escapes from the hospital and returns to the caves; after breaking his leg, he calls for help. In an undisclosed location, a man surrounded by clocks tinkers with a brass machine.

In 1986, Mikkel is visited in the hospital by a priest: Noah. After having discovered Ulrich and Katharina's affair, Hannah falsely tells Egon that she saw Ulrich rape Katharina, and Ulrich is arrested.

In 2019, Mikkel's family struggles not to turn against each other, Regina discovers that she has breast cancer, and Ulrich learns that his father was having an affair with Claudia at the time of Mads' disappearance. After learning that Regina was the last one to see Mads in 1986, Ulrich confronts her. While she admits to resenting him for bullying her during their childhood, she makes him see that Hannah was the one framing him for rape. Visiting the morgue, Ulrich finally realises that the dead boy is Mads, not aged since 33 years ago. Meanwhile, Jonas fails to tell his mother about the suicide letter but enters the caves armed with his father's notes and the equipment from the package sent by the Stranger. Within the caves, he finds a door with a Latin phrase, Sic mundus creatus est ("Thus the world was created"), and he goes through.

In 1986, Helge, who was working at the plant the night Mads disappeared, is questioned by Egon about his whereabouts. The Stranger explains to Jonas that Mikkel is indeed his father and warns him that taking Mikkel back home to 2019 will result in Jonas never being born. Katharina unsuccessfully attempts to convince Egon that Ulrich never raped her, and Helge and Noah prepare to move Yasin's dead body from a bunker behind Helge's cabin.

In 1953, birds begin to die, and the unidentified bodies of Erik and Yasin are discovered. Police chief Daniel Kahnwald (Ines' father) and officer Egon Tiedemann are puzzled by the boys' odd outfits. Ulrich arrives from 2019 and meets several locals, including newcomer Agnes Nielsen and her son Tronte, who are about to rent a room in the Tiedemann house, and a watchmaker named H.G. Tannhaus, who disclaims knowledge of the book found in Helge's 2019 home. Through the young Ines and Jana, Ulrich learns of the two bodies, and when introduced to the 9-year-old Helge, he believes killing him will save the lives of the boys. He bludgeons Helge and leaves him for dead in the bunker. Later, Tannhaus finds Ulrich's smartphone.

In 1986, teenage Ulrich is released without charges, and Hannah secretly discovers that a newly arrived young man, who calls himself Aleksander Köhler, is living under a false identity. When Bernd admits that the hidden barrels contain byproducts of a small meltdown, Claudia secretly hires Aleksander to weld shut the door to them. In an argument with Helge (revealing that the abducted boys died from Noah's attempt to create a time machine) Noah states his mission to free humanity, likening himself to the Biblical Noah.

In 2019, Hannah blackmails Aleksander into destroying Ulrich's life. She lies to Katharina that Ulrich wanted to leave his family. Regina discovers the Stranger's research, and Jonas breaks up with Martha. Bartosz is approached by an elderly Claudia, his supposedly dead grandmother. Later, Bartosz meets with Noah and agrees to join him.

On the night of Mikkel's disappearance, Peter is visiting Helge's cabin when Mads' body suddenly appears. He calls Tronte to the cabin, and Claudia arrives, telling them to move the corpse.

In 1986, the elderly Helge is killed while attempting to stop his younger self by deliberately crashing his car into him. Jonas has also returned to 1986 to bring Mikkel back to 2019, but Noah and Helge kidnap him. Jonas wakes in the bunker, accompanied by the Stranger, who reveals himself to be the adult Jonas. The Stranger leaves to destroy the wormhole using the brass machine, which Tannhaus has completed from the broken version brought by the adult Jonas and Ulrich's smartphone. Claudia starts to read Tannhaus' book.

In 2019, Charlotte uncovers a 1953 article on Helge's kidnapping, including a photo of Ulrich. Noah tells Bartosz that Claudia is their main adversary, and that the adult Jonas, unwittingly, is about to create the wormhole.

In 1921, a young Noah and another man are building the passage that will become the portal. Noah kills the other on suspicions that he "lost faith". The younger Noah is guided by his older self, a member of a society of time travellers called Sic Mundus led by the disfigured and mysterious Adam. Adam tells adult Noah to retrieve Claudia's diary in preparation for an "apocalypse" that will occur on 27 June 2020.

On 21 June 2020, six days before the apocalypse, things in Winden have grown tense. An investigator, Clausen, arrives to help Winden's police investigate the disappearances, which now include Helge, Jonas, and Ulrich. Katharina searches the cave for answers. Martha breaks up with Bartosz, who is now working with Noah. The adult Jonas from the future reveals his identity to Hannah. Aleksander has a truck of radioactive waste moved into the power plant.

In 1987, Mikkel struggles to adapt to life with Ines. Old Claudia visits her younger self, giving her coordinates of a time machine buried in her backyard. Egon has retired and begun to doubt his actions regarding the dead children's bodies in 1953. He interviews Helge (who tells him about a White Devil) and goes to the local psychiatric facility to visit an elderly Ulrich, who has spent 34 years incarcerated. Ulrich rebuffs Egon for his naivety.

In 2020, Clausen and Charlotte interview Regina, who is slowly dying from cancer. She discusses the Stranger who left his belongings at her hotel, which included pages from Tannhaus' book. The newfound evidence makes Charlotte, who was raised by Tannhaus, question her origins. Adult Jonas informs Hannah about time travel and takes her to 1987, where they see Mikkel in Ines' house.

In 1954, a young and disfigured Helge returns but refuses to talk to anyone but Noah, with whom he spent the last seven months in 1987 building a new time machine. Doris cheats on her husband, Egon, with Agnes. The elderly Claudia later meets with Agnes, a former member of Sic Mundus. Agnes meets with Noah, her brother, and tells him the location of the missing pages. Claudia delivers Tannhaus' book to him, then apologizes to her father's younger self, to his confusion. Claudia encounters Noah in the forest, who kills her. Noah retrieves the missing pages and is dismayed by his findings. He lies to Adam about finding the pages. Egon unsuccessfully interviews Helge and visits a catatonic Ulrich in jail.

An injured Jonas finds himself in Winden at the year 1921, where he is nursed by the inhabitants. He then tries to return to 2020 through the portal, but is stuck because the portal has yet to be built. Noah escorts him to meet Adam, who reveals himself to be an elderly Jonas.

In 2020, adult Jonas and Hannah meet Charlotte and Peter at the bunker and they discuss the existence of time travel, which they also reveal to a sceptical Katharina. The 1987 version of Claudia visits Winden's public library, where she discovers a report on Egon's death; she then travels back to 1987. Clausen interviews Aleksander, who reveals his original surname – Köhler – before he married Regina. Martha, Magnus, Franziska, and Elisabeth visit the cave, where they find Bartosz carrying the time machine. The kids take the time machine and leave Bartosz tied up in the cave. Katharina searches the school archives for the class photo of 1987 and identifies Mikkel, confirming Jonas' claims.

In 1921, Adam speaks with Jonas, who is dismayed by the callous person he is to become. Adam shows Jonas a God Particle that will take him to any time he wants. Jonas decides to go to the day before Michael kills himself to convince him not to do it.

In 1987, Claudia invites Egon to move in with her in hopes of preventing his impending death. Ulrich escapes the psychiatric ward to visit Mikkel at the Kahnwald house. After a conversation, Mikkel realises that the old man is actually his father. Ulrich tries to take Mikkel to the cave but is apprehended by the police.

Jonas travels back to 20 June 2019 to stop Michael from killing himself. Jonas' 2019 self goes to the beach with Martha, Bartosz, and Magnus; Mikkel unknowingly has a close encounter with his adult self; Charlotte and Peter struggle in the wake of Peter's affair; Aleksander fears his past will catch up to him. After witnessing his 2019 self leaving the lake, 2020 Jonas shares a kiss with Martha. 2019 Jonas and Hannah arrive at the Nielsen family home on Ulrich and Katharina's anniversary, where Jonas has sex with Martha and Ulrich starts his affair with Hannah. 2020 Jonas reconciles with his father as he tries to convince him to not kill himself. However, Michael states that he is not considering suicide and reveals that Jonas was the one who led Mikkel into the portal in the first place. After reading his suicide note, Michael suggests Jonas is really there to inform Michael of what he must do. The elderly Claudia arrives at the house and convinces them that Michael must die and Mikkel must travel to the past so Jonas can be conceived.

In 1954, Egon learns from the coroner that Claudia, discovered shot to death, had unusual amounts of radiation exposure. They theorize that she kidnapped Helge, but Helge says "he" told her about Claudia, the White Devil. Hannah travels to 1954 and asks to see Ulrich at the asylum. Ulrich promises he will leave Katharina for her if she helps him get out, but she does not believe him and coldly walks away.

In 1987, Claudia tries to prevent the death of her father. Egon deduces that she knows about time travel and is selfishly using the caves for her own gain. They struggle for the telephone and he falls and hits his head. As he dies, Egon tells her she is the White Devil. 2020 Jonas arrives and tells Claudia they still may be able to change the events.

In 1921, Noah tries to kill Adam for lying to him, but his gun fails to fire. Adam says he cannot be killed because that is "not his fate". He then explains that Elisabeth will become young Noah's wife and therefore Charlotte's mother, after which Agnes appears and kills Noah.

In 2020, young Jonas explains to Claudia that her elder self taught him how to save the world, whereas Adam wants to destroy it. Charlotte learns of the radioactive waste buried in the power plant; she believes that Clausen will provoke the apocalypse. Peter, Elisabeth, 1987 Claudia, Regina, and teen Noah take shelter in the bunker. Young Jonas and Martha reunite but are interrupted by Adam, who shoots Martha. In the power plant, Clausen opens the drums containing rocks soiled with dark matter.

In 1987, the "Unknown"—a time traveler appearing as his child, adult, and elder selves at the same time—burns down the Sic Mundus church, and later assassinates Bernd Doppler in his home, stealing the keys to the nuclear power plant.

Amidst the apocalypse in 2020, Jonas and the "other" Martha travel to a parallel world where Jonas was never born; Martha explains that this was the day she met him, then disappears. As of November 2019 in this alternate dimension, Katharina and Ulrich are divorced; Hannah is married to and pregnant by Ulrich, who is having an affair with Charlotte; Franziska is deaf instead of Elisabeth; and Regina is deceased. Jonas later meets an elderly Martha, who tells him that even though he does not exist in this world, it will nonetheless fall apart again and again.

In 1888, Franziska, Magnus, Bartosz, and adult Jonas learn about the second world from alternate-dimension Martha. The elderly Gustav Tannhaus – H.G. Tannhaus' grandfather – promises Jonas he can create a paradise. Bartosz shows Martha a secret lodge where Gustav's father Heinrich attempted to build a time machine. Martha reveals to Bartosz that Jonas is Adam.

In 1987, adult Katharina visits Ulrich in the psychiatric ward and promises to liberate him. Tronte's marriage with Jana is strained following Mads' disappearance and Tronte's affair with Claudia. Tronte visits Regina, who he believes is his child, and decides to stop investigating Claudia's disappearance. The Unknown breaks into the power plant and murders Claudia's secretary.

In September 2020, three months after the apocalypse, an ailing Regina is visited by the elderly Tronte, who reluctantly smothers her to death. Peter and Elisabeth learn that a perimeter wall will be built around Winden. They encounter the teenage Noah, who promises to protect Elisabeth.

In 1888, the Unknown murders Gustav Tannhaus. Bartosz clashes with Jonas, enraged that he did not disclose that he is Adam. Jonas tells Martha about Heinrich's attempt to build the time machine to prevent his wife's death. Martha gives Jonas dark matter for his God Particle machine, who then tries and fails to activate it. Martha uses the distraction to travel to 2053, where she is revealed to be taking orders from Adam.

In 1954, young Tronte meets the Unknown, who implies he is Tronte's father. Egon is having an affair with Hannah; she becomes pregnant and tells Egon, who gives her money for an abortion. While waiting, Hannah meets a young Helene Albers — Katharina's future mother. Hannah ultimately reconsiders and leaves. Jana begins to fall for Tronte, while Tronte loses his virginity to Claudia. Doris learns from the Unknown that Egon is having an affair; she decides to divorce him. The Unknown coerces Winden's mayor into approving the power plant.

In 2052 in the post-apocalyptic Eva's world, the adult Martha tells Jonas and young Martha they can prevent the apocalypse if they can stop the opening of the barrels in the power plant. After they leave, Noah of Eva's world appears and remarks that the Winden family lineage is an infinite circle. Martha and Jonas return to 2019 and have passionate sex.

In 1987, Katharina tries to rob Helene, who works at the psychiatric facility, to obtain her keycard. Helene bludgeons Katharina to death with a rock and drowns her body in the lake. H.G. Tannhaus reveals to the teenage Charlotte that she was given to him by two mysterious women shortly after his son, daughter-in-law, and granddaughter were killed in a car accident.

In 2020, Peter continues to look for Charlotte and Franziska, despite Elisabeth believing they are dead. Returning to their trailer, they encounter an intruder who murders Peter before being killed by Elisabeth. She goes to the cave and is comforted by Noah. Meanwhile, Claudia is met by her doppelgänger from Eva's world, who assigns her to save both worlds and gives her the journal for the first time.

In 2020, Claudia and Jonas — apparently still alive — go to the abandoned power plant and find the God Particle in a dormant state. Claudia persuades Jonas to help her restore it.

In 2052 in Eva's world, Eva explains to the young Martha who just killed Jonas that Martha's death in Adam's world is the point at which two parallel realities overlap in quantum entanglement: in one scenario, alternate Martha saves Jonas from the apocalypse; in the other, Jonas survives on his own, eventually becoming Adam.

The young Martha of Eva's world travels to the day of the apocalypse. Unable to reach Aleksander, she and Bartosz race to the power plant, but are intercepted by the adult Magnus and Franziska from Adam's world, who send Martha on her mission to rescue Jonas. Bartosz encounters his adult self, sent by Eva alongside the other acolytes of Erit Lux (transl. Let There Be Light, her world's counterpart to Sic Mundus). The Unknowns travel to the year 1986 in both worlds to release radioactive waste at the power plant – this eventually causes the wormhole and the apocalypse. Aleksander and Charlotte open the barrels at the power plant, unleashing the apocalypse in Eva's world.

In one scenario of the 2020 apocalypse, Martha from Eva's world saves Jonas; in the other, she is stopped by Bartosz of Eva's world. He takes Martha back to Eva, who instructs her to kill Jonas when he arrives with the other Martha.

In 1890, Bartosz meets Silja, who was sent from 2053 by Adam. They go on to have two children together: Hanno (Noah) and Agnes (whose birth results in Silja's death). In 1911, Hannah arrives with her daughter Silja to stay with Jonas, who has begun to transform into Adam. Jonas murders Hannah and sends Silja to post-apocalyptic Winden.

Jonas and Claudia work fruitlessly to reactivate the God Particle through 2041, by which point Charlotte has been born to Noah and Elisabeth. The adult Elisabeth and Charlotte from 2053 travel to 2041, kidnap baby Charlotte, and deliver her to Tannhaus. Noah's search for his daughter leads to his initiation into Sic Mundus by Adam in 1920. Claudia kills her counterpart from Eva's world and begins posing as her for Eva, all the while collecting information about both worlds. In 2052, the elderly Claudia sends the adult Jonas on his 2019 mission to Winden.

Claudia - who used the Apocalypse's quantum entanglement to get to 2053 - explains to Adam how he and Eva are locked in an inextricable triquetra knot that originated outside both their worlds. Claudia directs Adam to prevent the origin in a third, original world where H.G. Tannhaus created a time machine to prevent the death of his family, inadvertently destroying his world and splitting it into the worlds of Adam and Eva.

Using quantum entanglement, Adam returns to the Apocalypse and takes young Jonas to Eva's world, urging him to collect Martha and prevent the origin. Adam then confronts Eva and, to her shock, refuses to kill her as she remembers discovering. Recognizing that the cycle has been broken, Eva embraces Adam. Jonas and Martha travel to the origin world through the passage in the cave and successfully save Tannhaus' family, thereby erasing both worlds from existence.