Season 3

Complete listed story — includes the ending

1. Mother

In 2163, Cole finds Titan, just before it travels to 2047. Before he can try to rescue Cassie, he is splintered away by a future version of himself. Future Cole tells him to abandon his search for Cassie and look for Jennifer in the early 20th century. Future versions of Cassie and Cole speak briefly about the path present-day Cole must travel. In 1917, Jennifer has a vision of the Four Horsemen of the Apocalypse—four members of the Army—carrying a mysterious box. In 2163, Cassie is pregnant and in captivity, watched over by Magdalena, an Army member tasked to ensure she stays healthy to give birth to the Witness. Cassie escapes with the help of a maid, Arianna, and leaps off a ledge, hoping to kill herself and the Witness. Magdalena uses a wearable time machine to splinter back and alert her past self, who kills Arianna, preempting Cassie's escape. Several months later, Cassie gives birth to the Witness.

2. Guardians

In 1922, Jennifer enacts one-woman shows in a Paris theater, hoping Jones will notice them in the future in historical records and rescue her. When one of the Horsemen tries to kill her, Cole and Jones splinter in and kill him, then search for the other Horsemen. In 2046, Olivia takes Ramse to an adult Sam, who is near death from an attack by the Witness's men. Sam makes Ramse vow not to undo his death via time travel and to help Olivia kill the Witness; then Ramse euthanizes him. In 2047, Cassie watches as her infant son is placed in the mysterious box—his cradle—and splintered to 1922 with the Four Horsemen. In 1922, Cole and Jones kill two of the remaining Horsemen, and Cole comes upon the Witness's cradle; however, the fourth Horseman, Magdalena, splinters back in time to warn her past self of Cole and Jones's intervention, allowing her to reset the timeline and undo everything that happened after Cole and Jones arrived in 1922. Cole, Jones, and Jennifer then splinter back to 2046. Jennifer accepts Cole's offer to stay in 2046. Ramse brings a captive Olivia to the temporal facility, shouting for Cole.

3. Enemy

In 2046, Jones has Olivia imprisoned and interrogated. When the latter fails to talk, Jones tortures her by locking her into a time loop where she is splintered repeatedly in and out of existence. Seeing it is not working, Cole instead travels three months back in time with Olivia and confines her in a dungeon reminiscent of the "box" she grew up in. Afterwards, a seemingly broken Olivia agrees to tell them how to find the Witness. In 2047 in Titan, Deacon is brought back from the brink of death by Mallick, one of the Army's enforcers. While he recuperates, he argues with a hallucination of his dead, abusive father about his life, his brother, and the person he became. When he is fully healed, Mallick has him free Cassie from the Army. Back in 2046, Jones sends Cole and Ramse to 2007 to kill the Witness. It is revealed that Olivia told Ramse about the Witness's parentage and that she turned herself in to Project: Splinter in order to manipulate Jones into sending Ramse to 2007 so that he can fulfill his true, secret mission: killing Cassie.

4. Brothers

In 2046, Jennifer has repeated dreams of an unidentified dying man in a church, and begins sketching her visions. Becoming suspicious of Olivia's motives, she questions the woman about her real reasons in coming to Project: Splinter. In 2007, Ramse maintains the charade that he and Cole are there to kill the Witness while secretly plotting to kill Cassie. After a first failed attempt, Cole inadvertently gives him information on her location. Ramse slips away from Cole and goes to the location, only to find Cole waiting for him, having deliberately misinformed Ramse after deducing his real target. Ramse tells a stunned Cole that the Witness is his and Cassie's son. The two argue, and Cole mortally wounds Ramse. Before he dies, Ramse reconciles with Cole and pleads with him not to use time travel to undo his death. In 2047, Cassie and Deacon escape from Titan with Mallick's help and make their way back to the temporal facility, finding it totally destroyed. Noticing a sign from the past left for her, Cassie unearths time-travel tethers that allow her and Deacon to splinter back to 2046, where they reunite with Cole.

5. Causality

In 2046, Cole and Cassie decide to keep the identity of their son, Athan, secret from Jones. Jones agrees to Jennifer's elaborate plan to obtain the Word of the Witness by splintering her to 1989 and posing as her own mother at an auction so that Cole and Cassie can get access to the Word and make a copy, then return it to its hiding place in order not to disturb the causal chain. The plan goes awry when Jennifer exceeds her bidding limit during the auction, causing Leland Goines to intervene and forcing Deacon to take the bidders hostage. When Cole and Cassie fail to find the Word, Jennifer manages to track it down and make a copy, briefly confronting her father and her 1989 self. Upon returning to 2046, Cole and Cassie fear the Word will reveal the Witness's true identity, but it is revealed Jennifer deliberately blotted out that portion of the Word when copying it.

6. Nature

In 2046, Jennifer's visions intensify, and on Deacon's advice, she begins conversing with them. Following a lead from the Word of the Witness, Cole and Cassie splinter to 1953, where they recruit FBI Agent Gale to help them. Gale learns that several locations mentioned in the Word are sites of disasters, and that people in those sites are disappearing. Cassie poses as a woman widowed by a mining accident to lure out the Army; a mysterious man makes contact and invites her to a revival gathering. Cassie tells Gale that she and Cole will be responsible for his death in 1961. At the revival, Cole and Cassie learn the mysterious man is a missionary; his wife is the female Messenger, Mantis, and his son is the Pallid Man. There, Athan, in this time a young boy, is revealed to be a Primary. He chooses one of the audience members to be initiated into the Army, then gasses the remaining audience to death. Cole and Cassie steal a personal time machine from a Horseman and escape back to 2046. Cassie tells Cole she cannot kill their son, even after seeing what he is; Cole replies that he can.

7. Nurture

In 2046, Jones learns how to disrupt the personal time machines and prevent the Horsemen from resetting the timeline. She sends a team to 1953 to kill Athan. Cassie requests to be sent instead to 1990, where she asks her mother, a psychiatrist, to analyze the Word of the Witness. The elder Cassie concludes its author is deeply uncertain of himself and loathes killing, reassuring Cassie Athan is not a monster. She returns to 2046, finding Jones has traveled in time to learn that the Witness is her and Cole's son. Furious at her betrayal, Jones imprisons Cassie, who steals the personal time machine and splinters to 1953. In 1953, Jones's team assaults the Army's hideout in pursuit of Athan. Hannah is severely wounded, and Jennifer briefly converses with Athan, Primary-to-Primary. Cassie kills Magdalena. When Cole is unable to bring himself to kill Athan, Deacon prepares to do so, but Cassie shoots him down, and Athan splinters away with a Horseman. Cole steals a personal time machine and splinters away with Cassie to search for Athan. The rest of the team returns to 2046, where Jones and Deacon prepare to hunt down Cole and Cassie.

8. Masks

In 1879, Sebastian, the Horseman who helped Athan escape 1953, encourages Athan to write his visions down in the document that becomes the Word of the Witness. In 2046, Jones has difficulty tracking Cole and Cassie as they jump through time. She consults Olivia, who tells her Jennifer is protecting them by misdirecting her. Before Jones can catch her, Jennifer splinters away. In 1899 London, Cole and Cassie attend a masked ball which was mentioned in the Word. They find Sebastian but are captured by Jones, Deacon, and Hannah. Cole unsuccessfully tries to convince Jones that Athan can be saved. Jennifer appears and creates a distraction, allowing Cole, Cassie, and Sebastian to escape. Sebastian says he and Athan parted in 1879 but gives them the address of Athan's old home. He is shot by Jones, buying Cole and Cassie time to splinter away to Athan's house. Back in 2046, Deacon imprisons Jennifer and releases Olivia. In 1899, an adult Athan bids farewell to the dying Sebastian.

9. Thief

In 1899 London, Cole and Cassie read Athan's journals to learn about his past. Cursed with the ability to foresee others' deaths, Athan constantly splinters from era to era to stay sane. Eventually his time machine malfunctions, stranding him in 1891 London. He falls in love with a doctor, Eliza, whose death he cannot foresee. When Eliza is killed, he repairs the machine and uses it to prevent her death, but she dies of another cause. Despite hundreds of attempts to avert her death with time travel, she always dies on the same day. Athan splinters to the 2000s to see Cassie for advice. Having just lost her first patient, she suggests time is a "thief," wishing for it to stop forever; Athan then decides to embrace his destiny as the Witness and destroy time so that he can be reunited with Eliza. In 2046, Jennifer struggles to make sense of her visions. She determines she must save the dying man she saw, who is linked to a mausoleum. Eventually, she has Jones send her "home" with the time machine. In 1891 London, Cole and Cassie confront Athan.

10. Witness

Cole and Cassie meet Athan in 1959, at the House of Cedar and Pine, and try to convince him he can choose his own destiny. Jones's forces appear, having been told the location and time by Olivia. Titan splinters in around the house. Jones shoots and apparently kills Athan, whose personal time machine splinters him away. Mallick takes Cole, Cassie, and Jones to meet Olivia, the Army's new leader. It is revealed Olivia and Mallick had conspired to manipulate the members of Project Splinter into finding and killing the Witness. Unexpectedly, Athan splinters in. A flashback reveals he had splintered to Jennifer in 2017. She had summoned medical help to save him, and he had spent a year helping her work with her visions before returning to 1959 to rescue Cole, Cassie, and Jones. The latter flee and return to 2046 while Athan confronts Olivia. He tells her she, not he, is the true Witness. Shocked, she kills him and gives orders that Titan be splintered to 2046 and the temporal facility destroyed. In 2015, Cole's father gives young Cole a cryptic note from Cole's mother.