Here's what happened to all the main characters after the timeline was finally changed in Syfy's 12 Monkeys. The series, which was loosely based on the 1995 science fiction film of the same name, focused on the efforts of James Cole (Aaron Stanford), a man from a post-apocalyptic future who travels back in time to stop a plague. The whole point of his original plan was to change the timeline, a move which would erase him from existence, save seven billion people, and provide all the characters with new, better futures.
Joined by Dr. Cassandra Railly (Amanda Schull) from the present, his best friend Ramse (Kirk Acevedo), brilliant scientist Katarina Jones (Barbara Sukowa), and more, Cole eventually discovered that their problems were much bigger than a plague. The plague was just one step in a much more complicated scheme to destroy time itself. The plan was orchestrated by a secretive group called the Army of the 12 Monkeys and their elusive leader, the Witness, who was eventually revealed to be a future version of one of the Witness' lackies, Olivia (Alisen Down).
In the last episode of 12 Monkeys season 4, the conflict between Team Splinter and the Witness came to a head in an epic showdown at the Witness' base, Titan. After the Witness was killed by Cassie, their chance to save the timeline finally came - but there was a cost. Cole, whose entire existence was a consequence of the future they wanted to prevent, had to be erased in order for them to achieve their ultimate goal. Once Cole was erased, 12 Monkeys' timeline was reset and the future was changed. A scene in the final minutes of the finale revealed the fates of Cassie and all the others. Here's what happened to all the main characters in the new timeline.
Cassie
Scenes that mirror the 12 Monkeys series premiere reveal that in the new timeline, Cassie's life went much the same way it did originally, with her being a respected doctor at the CDC - except this time Cole doesn't kidnap her when she gets her in her care after a lecture. Over time, Cassie recovers at least some of her memories of the mission to stop the Witness, and buys the same house that she and Cole lived in during the 1950s. Cassie eventually realizes that something is missing from her life, and slowly remembers Cole.
Ramse
Ramse's main mission in 12 Monkeys was to protect his son, and after going through a number of personal tragedies, Ramse was unable to save him. Eager for revenge, Ramse determined that he had to kill Cassie to prevent the birth of the Witness. This forced Cole to kill him in a 12 Monkeys season 3 episode. In the series finale, Ramse is shown playing the game "Go" with his son, which meant that Ramse still met Elena (Amy Sloan) at some point in his life, and had a child with her. But in this version of the story, Ramse doesn't get forcibly separated from his son.
Deacon
After being a villain in 12 Monkeys season 1, the leader of the West VII gang, Deacon (Todd Stashwick), evolved into a valued member of the team. He was tragically killed off in season 4 when he was beheaded by the Witness. All that changed in the new reality created by Cole and Cassie's actions. Deacon now runs a bar with his brother, who he often talked about fondly in the original timeline.
Jennifer
When Jennifer (Emily Hampshire) temporarily took over Markridge in 12 Monkeys season 1 and ranted about her wish to genetically engineer a unicorn, Jennifer insisted she was serious. This was proven to be true in the finale, because that's exactly what Jennifer did in the rewritten timeline as the CEO of Markridge. Cassie appears pleased when she sees a new broadcast that revealed to her how successful Jennifer has become. It's confirmed that Jennifer, like Cassie, regained her memories of their past adventures. Decades later, Old Jennifer can be seen at Deacon's bar, so it's possible that their connection was reestablished.
Agent Gale
FBI agent and recurring character Robert Gale (Jay Karnes) helped Cole and Cassie many times on their trips to the past, but what would happen to him in the long run wasn't clear. A deleted scene in the finale shows Cassie looking him up on the internet to find out his fate. Apparently, Gale became the director of the FBI and lived to the age of 81. He died in 1984.
Whitley
Sergeant Marcus Whitley (Demore Barnes) was Jones' most loyal ally from the very beginning of the series, all the way up to his death in the 12 Monkeys season 4 premiere. A deleted scene from the series finale provided a glimpse into Whitley's new life after the timeline reset. Whitley became an architect and started his own company. Being an architect was a dream Whitley briefly mentioned early on in the series.
Jones & Hannah
12 Monkeys season 4 killed off the entire Jones family. Hannah died shortly after the shocking reveal that she was Cole's mother, Elliot was killed by Deacon, and Jones died moments before Cole was ultimately erased. The altered timeline fixed all of this; it's revealed that Jones either stayed with or got back together with her husband Elliot (Peter Outerbridge), and the three of them remained a family. Jones never had to lose Hannah as a child, while Hannah never had to become Cole's mother, nor did she have to die saving him.
Dr. Lasky and Dr. Adler
The two main scientists who helped Jones with Project Splinter, Dr. Lasky (Murray Furrow) and Dr. Adler (Andrew Gillies), played key roles in helping Cole and Cassie save the future. Dr. Lasky met his end at the beginning of 12 Monkeys season 4, and Dr. Adler was killed in the final battle with the Witness. However, they both were present in the new reality. Somehow, the two even became friends, even though in this reality, they had no reason to know each other. It seems likely that the two remembered their experience with the Army of the 12 Monkeys.
Cole
Cole was surprised to discover that he still existed, even though he was erased. He found out from Jennifer that Jones programmed the machine to erase Cole from every point in the timeline, except for one. Since Cole's birth never happened, he is now an anomaly. Cole asked Jennifer how this could work, since this was just another attempt to manipulate time, but Jennifer said, "time knows". Jennifer explained that "Time" knows it owes this to Cole, because of everything that he did to save the future. So in 12 Monkeys' final scene, Cole reunited with Cassie, and the two characters - like everyone else - got to live "happily ever after".