HG Wells left to go find Clark before Lois and alternate Clark figured out the mind control device was in the phone system. HG Wells was later talking to Tempus and he told him alternate Clark would find the device in the phone system and destroy it but Wells wouldn't have known that's where the device was.
Tempus plots to flee to the alternate universe to escape the nuclear holocaust he is setting off, but he has no means of doing so. Both of Andrus's time windows were rendered useless to him in the previous episode, H.G. Wells said he had calibrated his time machine so that only he could operate it, and the previous episode made clear that Tempus has no independent means of moving between dimensions.