Omnitron-X (damaged) and Golem Unity combined (Theory, of course).
This explains the bunker (Omnitron as a factory) and the ability to send things through time (Omnitron-X's ability to travel through time). So this is the end of the timeline with Iron Legacy. They recognize the targets from the past (thanks to both of their 'databases') and they've known Haka for some time (Unity longer than Omnitron-X).
I don't have many more ideas than this, but I figured I'd throw this one out there.