Your memory's not playing tricks on you. I remember a scene like that. Clark is x-raying Luthor's tower to make sure he doesn't get away before Henderson arrives to arrest him. Unfortunately I can't for the life of me remember the name or the author and I can't find it after trying to search what may be relevant terms. Maybe someone else will have more luck. I've given some of the details of the rest of the story (unless I'm mixing it with another) in case someone else recognises it).
I'm pretty sure that the story was based around the pilot. Clark went with Lois and they break into Baines' office to look for files. Luthor enters the office and they hide but Lois takes a photo and he hears and then catches her. Clark makes judicious use of his powers to distract Luthor but they both end up caught. Luthor marches them out to the sheds (telling Clark that one movement from him and he'll shoot Lois - Lois is surprised that Clark stays). They're tied up with the bomb, they kiss and Clark whisks her out just as it explodes. She finds out about his powers and they go to report what happened.
Then the scene you mention comes in. They're worrying about how to track down Luthor when they realise that he still thinks they're dead and no longer a problem, with no one knowing the truth and so will probably be happily sleeping at home. Clark flies them over and they check, He is there so they phone Henderson and then stay to make sure he doesn't get away before the cops arrive. I'm pretty sure St John gets the drop on Henderson and Clark has to drop Lois off quickly and zip through with some assistance.
Hope someone knows this. It's bugging me now as I think I reread it not too long ago.
