Professor Moriarty happened to be waiting in the very observatory they materialized in, and stole the atomic clock that had brought them there. He managed to elude both the Turtles and his nemesis Sherlock Holmes, making his way to Oxford and adding the atomic clock as the final piece of his time machine.
With this time machine, he managed to make himself emperor of the world in the future, wrecking the timeline and changing the "present." He nearly outwitted the Turtles in their efforts to steal back the atomic clock, but they managed to restore the timeline. Moriarty was thrown back in time to his own era, without the clock.