Asking what is up with the ending of 12 Monkeys is like asking what started the big bang or how life came to Earth or why things act so weirdly at the atomic level. We may never know the answers to these questions, but they are fun to ponder nonetheless.
In other words, if you came here looking for a definitive answer to wrap up your discussion of the film, then sorry in advance.
Will the Circle Be Unbroken?
12 Monkeys' answer to this Christian hymn is a definitive yes. But let's back up a second and reconsider what exactly happened at the film's conclusion.
Desperate to stop Dr. Peters from boarding the airplane to spread the virus, Cole runs by airport security and draws the gun given to him by Jose. He's about to take his shot when the police show up and gun him down instead. Cole tumbles to the ground, arms outstretched, blood pooling in his shirt. Railly rushes to his side to comfort him in his last seconds, and…wait a minute. This all looks super familiar.
Yep, it's Cole recurring dream, this time in real-time. Turns out, his dream was a memory from his younger self, and we see a young Cole watching the drama play out before him. Railly sees this, too, and sadly smiles at the boy as she is dragged away by the police. Why she smiles is left a mystery, perhaps she smiles to reassure the boy; perhaps knowing that Cole will live on in some manner makers her happy in a bittersweet way
This ending wraps up the story's theme of fate in a nice bow. Actually, make that a time loop, not a bow. Cole was destined to die in that airport, and there was nothing he could do. Call it destiny or determinism, but no choice he could make would stop this from happening.
If you'll recall, Cole set up the idea of deterministic fate much earlier in the film when he told the psychiatrists: "How can I save you? This already happened. I can't save you. Nobody can." Nor could he save himself, it seems. Despite his best efforts and our hopes that maybe he could pull it off, the film landed on the side of determinism after all.
This scene also connects to the idea of Cole as a Christ-like savior (James Cole = JC, get it?). Notice that when Cole dies, his arms spread wide, resembling Jesus' arms as tied to the cross. Both men also live on after their deaths—Jesus because he is resurrected, while Cole lives through his younger self—and were destined to die in order to save humanity
But does Cole really save humanity? Or is his death another event that ultimately leads to humanity's extermination? Well, that answer depends on how you read the next scene.
With Cole dead and no one to stop him, Dr. Peters boards the plane with his deadly disease. He takes his seat, and the woman in the seat next to him starts a conversation:
PETERS: Excuse me.
WOMAN: It's obscene, all the violence, all the lunacy. Shootings even at airports now. You might say that we're the next endangered species. Human beings.
PETERS [panting]: I think you're right, ma'am. I think you've hit the nail on the head.
WOMAN: Jones is my name. [She shakes Peters' hand.] I'm in insurance.
The camera pans over and reveals the woman to be none other than the Astrophysicist. Now, there are a couple of ways to read this exchange, specifically that last line. We're going to discuss three of those ways.
First, she could be insurance in case the plan to kill Peters failed. With Cole dead, she boarded the plane to either kill Peters or secure a sample of the virus to take back to the future and study. Cole may have died, but he ultimately succeeded in his goal of "trying to gather information to help the people in the present trace the path of the virus." In this reading, he saves humanity even if he won't be around to see how great the statue is they built in his honor (we're guessing pretty great).
But there is another possibility. What if the Astrophysicist isn't Cole's insurance but Dr. Peters? Under this reading, the Astrophysicist is there to ensure that Dr. Peters manages to set off the virus and keep the world on the course that leads to the year 2035 we all know and hate.
Why would she do this? Well, she's part of an oligarchical elite in that future. In any other future, she may struggle to make ends meet, but in that hellhole, she's running the show.
The third possibility is that the woman on the plane isn't the Astrophysicist at all. She really is just a woman name Jones who works in insurance, and Cole was crazy all along. The fact that you thought she was the Astrophysicist just proves that you, the viewer, have bought into Cole's delusions like Dr. Railly. In the end, you're as nutty as a monkey!
After all this brain exercise, we could really go for a banana about now. You know, get some potassium to prevent brain cramps.