Scully begins to accept that Mulder and Morris have switched bodies. The question is, can anything be done about it?
Close Enough Timeline: Everything gets set back to normal and the whole universe goes back to the way it was before the time rip — but Mulder's apartment is still cleaned up and has a waterbed, and Scully still has a dime and penny that were fused together by the warp in space-time, even though the events that caused both scenarios never happened.
Ontological Inertia: Played with. If they can be in the right place when the snap-back happens, Morris and Mulder will get sorted out like the pilot and the old woman did, complete with a Reset Button resulting in it being "like the past few days never happened." The fused coins and the waterbed, however ...
Something Else Also Rises: Morris Fletcher as "Mulder" tries to seduce Scully. He holds a bottle of champagne in his lap which pops open and overflows.
Trademark Favorite Food: Mulder as "Morris" puts a handful of sunflower seeds into Scully's hand, further proving he really is Mulder.
The Un-Reveal: When Mulder finally gets to speak with his confidential informant, the informant reveals... that he has no idea what the true nature of their work is. Nobody at Area 51 knows what the experimental aircraft are, they simply test them. He called Mulder in the hopes that Mulder could tell him if aliens actually exist.