We get it. Time travel can be confusing, so here's a timeline that features ALL the Season 3 time jumps, to help you keep track.
12 Monkeys Timeline
Cassie and Cole chase The Witness (Athan) through time
The Witness (Athan) is a young adult, having been raised in different time periods by the sole surviving Guardian of 1953’s massacre. Athan starts writing the Word of the Witness.
The now adult Witness (Athan), having travelled and lived through countless decades, meets a woman named Eliza. Athan falls in love with her, but she later dies. Athan is crushed, and we see why he became someone that wanted to destroy time.
Cassie and Cole come face to face with Athan, who flees through time.
Cassie and Cole are nearly caught by Jones (but saved by Jennifer) before getting a vital clue on the Witness’ (Athan) location.
Thanks to the events of the Season 2 cliffhanger, Jennifer is stuck in France during World War I.
Jennifer, still stuck, writes postcards for Jones and Cole to find in the future in hopes of rescue. She also starts performing in one-woman shows.
Magdalena arrives from five months later to warn the guardians of the Witness of Cole’s arrival months later. They immediately leave France, altering the timeline so that five months later Cole, Jones and Jennifer never encounter them.
Off future Cole’s advice, Jones and Cole rescue Jennifer from France and encounter the four guardians of the Witness. Some die, but one, Magdalena, travels months earlier to warn her earlier self of James’ arrival. Because of that, the guardians leave months earlier and the timeline is altered.
Cassie and Cole chase The Witness (Athan) through time.
Deacon and Hannah, Jones’ daughter, almost catch Cassie and Cole, who are traveling through time looking for their son
Cole steals a prototype of a time travel suits which Jones soups up. The wearer can travel through time without the machine.
With guidance from the Word of the Witness, Cole and Cassie arrive and discover that Mantis (the mother of the Pallid Man) and a man named Zaimon Shaw have started the Army of the 12 Monkeys by promising family members of the dead an escape from their pain. Zaimon introduces the Witness to the assembled crowd. Cassie and Cole see their son for the first time.
Cole prepares to kill the child Witness, but finds that he can’t. Cassie arrives. One of the Guardians transports the Witness away. Cole steals a time machine suit from one of the dead Guardians. He and Cassie set out to locate their son.
Having caught The Witness (Athan), Cole and Cassie bring him to the place of his conception to get through to him. Jones arrives and shoots Athan, who splinters away. Jones, Cole and Cassie are kidnapped by Olivia, who has killed the Pallid Man and performed a coup of the Army of the 12 Monkeys.
Just as Olivia is about to murder Jones, Cassie and Cole, The Witness (Athan) arrives from 2018 and saves them. They splinter away. Athan reveals to Olivia SHE is actually the Witness and her future self will engineer all the events the Witness has thus far. Olivia murders him.
Jennifer, Deacon, Cassie and Cole arrive to make a photocopy of the Word of the Witness so they can locate him.
An adult Cassie visits her mother, who died years later. The conversation makes her realize she wants to save, not kill, her son (The Witness)
Ramse and Cole arrive from the future. Cole quickly realizes that Ramse wants to kill Cassie and that the Witness is his son. He kills Ramse to save Cassie. Jones, suspicious of Cole when he comes back without Ramse, travels back there and overhears that the Witness is Cole's son.
Jennifer finds The Witness (Athan), having been gravely wounded by Jones in 1959. She nurses him back to health
Cassie and Cole chase The Witness (Athan) through time
With the plague having begun, a healed Witness (Athan) heads back to 1959 to save Cole and Cassie
Ramse, off the events of Season 2, is with Olivia who reveals that she has his son, Sam. Apparently when Sam was splintered by the Witness in Season 2, he was shuttled from 2044 to 2023, where Olivia found him and raised him. A wounded Sam dies with Ramse by his side.
Jones, Jennifer and Cole return from 1922 and Ramse reunites with Cole. Olivia tells Ramse that the Witness is Cole and Cassie’s son, and encourages him to go back in time to kill Cassie before she ever met Cole, thus preventing the Witness’ birth. Ramse tricks Cole into returning to 2007 with him.
Cassie and Deacon, fresh off the time travel injections from their escape from Titan, arrive. They bury the injections that they'd later find in 2047.
Cassie returns from 1990 and Jones confronts her about being the Witness’ mother. Cassie steals the time travel suit and travels back to 1953.
Deacon takes pity on Jennifer, who has been locked up since helping Cole and Cassie in 1899, and agrees to send her home
Olivia escapes from the facility and heads to Titan, where she stages a coup of the Army of the 12 Monkeys
Cassie, Cole and Jones return from the showdown with Olivia in 1959.
Deacon, a prisoner in Titan since the end of Season 2, finds Cassie, rescues her and they escape. They find the ruins of the Temporal Facility, but some buried time travel injections that were clearly left by the team in the past, knowing that Cassie and Deacon would arrive and need them.
Cole, followed by Jones’ daughter Hannah, searches different locales in hopes of locating Titan and Cassie.
A future version of Cole (with a future version of Cassie lingering in the shadows) abducts Cole-from-Season-3-looking-for-Cassie-in-Titan and tells him that Jennifer, trapped in the past, is the way to find Cassie.
Cassie gives birth to the Witness