Season 2

Complete listed story — includes the ending

1. Year of the Monkey

In 2016, Cole and Ramse are on the run from the Army. They ask Benjamin Kalman, an ex-Markridge scientist, to remove a tracking device from Ramse. Kalman, who is still in the Army's employ, paralyzes Ramse and reveals that Jennifer Goines will release the plague in New York. Cole disposes of Kalman, and Ramse decides to accompany him to New York to find Jennifer. In 2043, the Messengers, the mysterious group of 12, use the time machine to send 6 of their members to other times. Cassie, now imprisoned by the Messengers, offers to treat Deacon's chronic illness if he helps stop them; he frees her and has the West VII blow up the time machine, killing the remaining Messengers. Back in 2016, Cole tracks Jennifer down and urges her not to release the virus. Agents of the Army interrupt and attempt to kill Cole, but Cassie splinters in from 2044 and shoots them, telling Cole that she and Jones deduced that Jennifer started the plague. She prepares to shoot Jennifer, but Cole raises his own gun to stop her, ending in a standoff.

2. Primary

In 2016, Cole persuades Jennifer not to release the plague. He and Cassie destroy Jennifer's supply of virus, altering history, although they, Ramse, and Jones still remember the previous timeline thanks to the time-travel drug. After Cole stops Cassie from killing Ramse, she splinters to 2044 with the latter, abandoning Cole in 2016. Jennifer takes Cole to the Emerson Hotel, where the manager gives Cole the key to room 607, which Cole purchased in 1944. Inside, Cole finds a photo of him and Cassie from 1944. Jennifer, feeling purposeless after deciding not to start the plague, attacks and seduces Cole, then cuts herself. Cole calms her and tells her to find a new purpose, and she leaves. In 2044, history has changed: the plague began a few years later, and Jones has a lover, Dr. Eckland, of whom she has no memory. Deacon and Cassie unsuccessfully interrogate Ramse about the Messengers. The older Jennifer has the Daughters force Jones to retrieve Cole from 2016, repaying him for helping her younger self. Cole talks with Cassie about how his actions have affected her and how saving, not killing, people is the only thing he has done that changed history. He leaves Cassie to contemplate the 1944 photo.

3. One Hundred Years

Cole and Cassie travel to 1944 to stop two of the Messengers from murdering a scientist, Thomas Crawford. They are unable to prevent Crawford's death but deduce that the Messengers' real target is his son Tommy Jr., who, like Jennifer, is a "Primary" with a special connection to time. They manage to get to Tommy first; he addresses both of them by name and says he is fated to be killed by the Messengers. One of the Messengers takes Cole hostage and tortures him, forcing Cassie to surrender Tommy. The Messenger kills Tommy in a ceremonial ritual using bone taken from his remains in the future, triggering an explosive temporal paradox that renders her, Cole, and Cassie unconscious and strands the latter two in 1944. In 2044, Jones allows Deacon to do as he wishes with Ramse. Just as he is about to kill Ramse, a massive temporal anomaly erupts, and Ramse runs to escape it, dragging Deacon along with him.

4. Emergence

Ramse is sent to 1944 to rescue Cole and Cassie. Though unable to stop Tommy's murder, he frees them from FBI agent Robert Gale. Gale deduces Cole is a time traveler and lets him interrogate the female Messenger who killed Tommy. She reveals that the Witness seeks to destroy time itself, then escapes. After the three travelers return to 2044, Gale leaves Cole and Cassie's photo in the Emerson Hotel for Cole to find in 2016. In 2044, a baffled Jones turns to Jennifer for help as the temporal anomaly grows. In a drug-induced vision about the nature of time, she learns that the Army plans to destroy time by killing the Primaries. Upon returning, Cole, Cassie, and Ramse grudgingly agree to work together to save the Primaries. In 1971, the female Messenger dies after inducting her son, the Pallid Man, into the Army. In 2016, Jennifer checks herself into a mental clinic as the Pallid Man watches outside.

5. Bodies of Water

In 2044, Jennifer sends Cassie to 2016 to get the Primaries' identities from her younger self. Desperate to get rid of Deacon, Cole and Ramse betray him to one of his enemies, the Foreman. Deacon kills the Foreman, and instead of retaliating, congratulates the duo on becoming as ruthless as he. In 2016, the Witness gives Olivia a new mission: find and prepare Cassie. Cassie and Jennifer return to the latter's old home, which triggers childhood memories of Jennifer's mother trying to drown her. Cassie comforts Jennifer, who is then able to tell Cassie another Primary's name: Kyle Slade. The Pallid Man captures them, and Olivia gives Cassie a hallucinogen. In a vision, Cassie sees Aaron's face behind the Witness's mask. Jennifer breaks loose and sees a manuscript, "the Word of the Witness," containing her death date: September 23, 2044. She rescues Cassie and stabs Olivia. The Witness puts the Pallid Man in charge of the Army's mission, replacing Olivia. Cassie tells Cole about Slade and decides to stay in 2016 to look after Jennifer. In 1975, Slade senses that Cole is coming for him.

6. Immortal

Cole and Ramse travel to 1975 to prevent the Messengers from "paradoxing" Kyle Slade, a Vietnam vet turned serial killer. They rescue Victoria Mason, Slade's last recorded victim, then tip off the police who arrest Slade. However, Slade claims that he knows where the Witness is, so Cole frees him, abandoning Ramse. A Messenger holds Victoria hostage, and Ramse kills him and frees her. Slade tells Cole his victims were Primaries whom he killed to stop the Army from sacrificing them and leads Cole to his lair, where he is holding captive a man he claims is the Witness. Cole recognizes the man as a Messenger, not the Witness. Realizing Slade is completely insane, Cole and Ramse kill the Messenger, then Slade. Upon their return to 2044, the temporal anomaly has partially receded. In 2016, Cassie sees the Witness, who appears to her in a vision as Aaron, then as Cole. Jennifer leaves Cassie to look for other ways of fighting the Army. Cassie is left questioning her sanity as she continues to have visions of the Witness.

7. Meltdown

In 2044, Cassie's hallucinations worsen. The time machine suddenly malfunctions, transporting people from random points in the timeline into the temporal facility, including soldiers from 1959 and horribly mutated former test subjects for Project Splinter, with whom the team members are confronted. Eckland sacrifices himself to prevent the time machine from destroying the facility. When Cole and Ramse try to power down the machine, Cassie takes Sam hostage and holds him at gunpoint to stop them. Cole and Ramse realize she is under the influence of the Witness, who used her to sabotage the machine. To snap her out of her trance, Cole has Ramse shoot him, knowing she will not let him die. Ramse shuts down the power, but Sam is struck by a backlash of temporal energy and splinters. Jones administers Cassie a drug to prevent the Witness from possessing her again, and a grieving Ramse leaves the temporal facility. Sam is met in an unspecified time period by an unseen figure.

8. Lullaby

Despondent over Eckland's death, Jones sends Cassie to 2020 to assassinate her younger self and prevent Project Splinter from ever beginning. There, Cassie finds the Jones of 2020 watching over her deathly ill daughter, Hannah. After she kills Jones, Cassie wakes up at the beginning of the same day, along with Cole, who has come to stop her. Eventually they discover they are trapped in a temporal loop. With help from the Jennifer of 2020, they break the loop and return to 2044. They explain to Jones that her creation of Project Splinter was fated and attempting to alter that fate caused the loop. To escape it, they saved Hannah and gave her to Jennifer's Daughters to raise, letting Jones believe she was dead so that she would start the project. They then reunite Jones with the adult Hannah. Cole tells Cassie about his feelings for her, but she rebuffs him, fearing that they stand to lose too much if she reciprocates. Ramse appears in her room, threatening to shoot her for her role in Sam's disappearance. Instead she proposes that the two of them kill the Witness; he agrees.

9. Hyena

In 2044, Cassie and Ramse search for an archivist known as the Keeper, hoping to learn about Titan, a place linked to the Witness. He points them to a Dr. Kirschner in 1961 East Germany. Cole travels to 2016 to meet with Jennifer, who now leads the Hyenas, a group of former psychiatric patients whom she gathered to fight the Army. The Hyenas capture Oliver Peters, who has created a vaccine for the plague virus, and use him as bait to lure out the Pallid Man. The Hyenas eventually turn on Jennifer and Cole, who manage to capture the Pallid Man and run away from the Hyenas. Cole tortures the Pallid Man for information on the last Primary; he says the final paradox takes place in 1957 New York. He then reveals he let himself be captured in order to get to Jennifer and detonates a bomb which kills Peters and all the Hyenas, then escapes. After consoling Jennifer on the Hyenas' deaths, Cole splinters away, and she finds another version of Cole at her door. The Pallid Man hires Dr. Elliot Jones, Jones's ex-husband and inventor of the time machine, to work on a project called "Titan."

10. Fatherland

In 2044, Ramse and Cassie go rogue and manage to trick Jones into sending them and Cole to 1961; once there, they drug Cole and go to East Berlin, where they find Nazi war criminal Dr. Kirschner but are captured by Mossad agents. Cole enlists the help of FBI agent Gale to help him rescue Cassie, Ramse, and Kirschner. The group realizes that Kirschner is the member of the Army who created the Messengers. Gale sacrifices himself to help the others cross the Berlin Wall. In his West Berlin laboratory, Kirschner shows them the Word of the Witness and reveals the fruits of his research: a young Olivia, who was created using Mantis's ova. Mantis arrives with a group of Army agents to take Olivia, and Kirschner is killed. As the three time travelers are splintered back to 2044, Ramse tears off a corner of the Word of the Witness relating to Titan. Mantis then inducts Olivia into the Army, revealing that the Pallid Man is Olivia's brother. In 2016, Olivia abandons the Army, feeling betrayed by the Witness. Back in 2044, a furious Cole has Ramse and Cassie arrested for going rogue.

11. Resurrection

In 2044, the temporal storms threaten to destroy the Project Splinter facility. Ramse, Cassie and Adler are set free by Whitley, and together mount a coup against Jones and Cole, hoping to use the time machine to travel to Titan and directly confront the Witness. Cole recruits Deacon's help, and persuades Jennifer and the Daughters to help retake the time machine so he can go to 1957 to stop the final paradox. In the process, Jennifer is fatally shot and Deacon is wounded. Cole retrieves young Jennifer from 2016, and 2044 Jennifer tells her younger self that she will have a choice: to lead the Daughters to Titan to battle the 12 Monkeys, or to lead them to find refuge, hoping Cole will succeed in his mission. As the older Jennifer dies, her younger version decides to go to Titan with Ramse's group and the Daughters. As the others evacuate the facility, Cole splinters to 1957; at the last minute, Cassie changes her mind about Titan and chooses to go to 1957 too. The temporal storms finally consume the temporal facility, including Jones and the machine.

12. Blood Washed Away

In 2044, the Project: Splinter members and the Daughters have grown weary of looking for Titan. One of the Daughters rebels and challenges Ramse to a duel to the death, but Jennifer intervenes to stop Ramse from striking the final blow. The group finally finds Titan and confronts the Witness. In 1957, Cole and Cassie spend a year searching desperately for the final Primary. After identifying a likely candidate, they find they have been tricked by one of the Messengers, who has fallen in love with and married his target, the final Primary. The Messenger stabs his wife with her bone and triggers the last paradox. The explosion knocks Cassie into a coma for over six months. When she finally awakes she finds Cole has bought the house she has seen many times in her visions of the Red Forest. There, the pair consummate their relationship while in 2044, the Witness's guardians ambush the Project members at Titan, killing them.

13. Memory of Tomorrow

With no way back, Cole and Cassie build a life together in the house from the Red Forest visions, and Cassie becomes pregnant. Cole experiences time freezes leading him to Lillian, a Primary who teaches him to use red tea, made from the leaves of plants affected by temporal anomalies, to untether his consciousness from time to stop the 1957 paradox. He does so, reluctantly erasing his timeline with Cassie, returning them to Jones in 2044. The three splinter spatially to Titan and with Jennifer and the Daughters prevent Ramse and Hannah dying. They realize Titan is a vast time machine as it activates around them. In the chaos, Deacon dies saving Jennifer who splinters to the trenches of World War I after being hit by a beam from Titan's time machinery; Ramse follows a rogue cell of the army led by Olivia who has custody of Sam; Cassie, now re-acquiring memories from her timeline with Cole, is captured within Titan as it splinters; and Cole demands to follow Cassie to an uncertain 2163. In 2163, Cassie is brought before the assembled Army where The Pallid Man hails her as the mother of The Witness.