Despite the overlapping and cyclical nature of time in the show, the series finale presents two distinct timelines that exist:
A) With James Cole
The events of the series, up until the last few moments of the series finale, occur in this timeline. With James Cole's existence, the Kalavirus, Red Forest, Witness, Project Splinter, etc. also exist.
B) Without James Cole
Though a version of James Cole does exist in this timeline after being splintered directly into 2018, he was never born and has no history. From the perspective of time itself, he does not exist. As a result, none of the events of the series occur.