None of what happened in the movie is real
Cole is in fact a schizophrenic patient, but the only parts of the film we see happen in reality are the scenes where he is in the hospital talking to psychiatrists. Both the "present" and future worlds were artificially constructed in his head. As a child, he was traumatized by an airport shooting, which in turn led to him constructing a world in his head. The psychologist Dr. Railly is real, and has been helping Cole for some time, but she is only going along with his delusions and occasionally having a bit of fun along the way (being able to leave a prank call about the Twelve Monkeys). Ultimately, Railly's help has started to bring Cole back into reality, but he is still under the delusion that he is a time traveler and requires her assistance, but occasionally he experiences a temporary relapse (his apparent returns to his own time). The climax is ultimately Cole coming to face the source of his delusions by experiencing the shooting again and confronting his delusions which, though not shown in the film, finally bring him back into the true reality.
Cole will get trapped in 2015 by the end of the first season.
The psycho band of scavengers introduced in S 01 E 03
will succeed in locating and storming the compound led by Jones. In the chaos, the time machine will somehow get damaged and prevents Cole from splintering into another time period.
Cole will discover that the plague was a result of a Stable Time Loop.
His own actions in the past will turn out to have set the plague and/or its instigators in motion, forcing him to splinter one final time to stop the splintering program before it can get started.