Lost In Time, Lost In Space

The two heroes had thwarted all of his evil plans, so after another last second escape, he planned, and he used his master stroke.

One of them, he stuck in space, lost in time, and the other he stuck in time, lost in space. Forever separating them, and ensuring he could carry out his diabolical plans in peace.

Except...

He didn't really think through having someone able to see all of time freely, having another able to be anywhere at one point in time, and the two able to meet up, communicate, and just keep changing the timeline for good.