I suspect that when the Professors finally unravel all of the plot threads, everything will make sense, but in a non-linear way.

It may be that all the villains are a single Other, in multiple bodies and at multiple times.

In fact, due to time travel and causal loops, the Other may not have had an actual beginning or an actual end, in which case the Good Guys would only hope that there is some point in time past which the Other did not venture.