Okay, I came up with another scenario that I like, and probably would have used if I hadn't already pledged not to make "Wrong Clark" another baby-involved epic...
Clark and Superman disappear after the first mission to battle Nightfall. Instead of landing in Metropolis, he returns to Smallville. So, when Luthor invites Lois to stay inside the ark, she agrees (BTW: this happens at least 24 hours before the second Nightfall piece is due to impact). Lex leaves Lois alone in the ark to get situated while he fetches (or orders someone to fetch) her belongings, not letting her leave in case she changes her mind.
Lois wanders around and finds a locked door, which of course, draws her curiosity. After picking the lock, she discovers the Vatman clone and thinks that it's Clark and that Luthor is holding him prisoner. (No slicked back hair, no Suit, so she doesn't think of Superman.) She frees Vatman from his cage and takes him back to her fake-apartment. They make love, with her believing the whole time, that this is Clark.
When Lois tells him that Lex is holding her prisoner, too, and about the asteroid, Vatman confesses that he's really "Superman". Lois convinces him to stop Nightfall, so he busts them out of the ark (up the elevator shaft?) and they return to Clark's apartment where they search and find Clark's uniforms. Vatman puts one on and goes to save Earth from Nightfall. Out of spite, he sends a piece of the asteroid down to destroy LexTower (or the building above where he was kept prisoner in the ark), killing Lex, Nigel, and Dr. Leek, and destroying access to the bunker. But this last bit of revenge, used up his last bit of super powers, (due to his imperfect clone DNA and therefore, having become vulnerable, or something), and he dies, never returning to Earth.
Afterwards when Clark doesn't return to Metropolis, Lois contacts the Kents. They tell her he is with them and that he has amnesia. Lois confesses to the Kents that she knows that he's Superman and that they had begun a relationship right before he left on the mission. The Kents don't realize that Lois meant this last mission, and she doesn't realize this isn't the same man she found down in the ark. She thinks that this amnesia came from his most recent battle with Nightfall. Lois heads out to Kansas and Clark, of course, falls in love with her at first sight (second sight?). She convinces the Kents to let her bring Clark back to Metropolis and see if being around familiar stuff there will bring back his memories.
Clark remains in her care in Metropolis and she takes him under her wing, teaching him the ropes at the DP, and hoping that the familiar surroundings bring back his memories. It is only after Lois announces that she's pregnant with his child that Clark recovers his memories. He's so happy that he and Lois are together, and that she's pregnant with his child, he doesn't question the timing much at first. But as time wears on, and facts -- he doesn't remember, but Lois does -- don't add up, Clark realizes that something is wrong.
At sometime in the future, while visiting the Prometheus space station or getting rid of a bomb or something, Clark discovers the lifeless dead body of Vatman floating in space.
