OK hold on.
So if you go with the idea that Cole is The Witness, we have to accept that it has always been Cole who has dictated the events that unfolded.
This includes giving comands to the 12 monkeys, etc.
For this to be possible, the current Cole would need to develop a motive between now and then...
Does he perhaps hear of the death's in 2044, and decide the only way to save them is to help Time reach that point, using the knowledge of what he's witnessed?
Afterall that's exactly what the witness has done, until we reach the point where he kills them all.
Que the time line altering change of fate where he saves them instead...
