I'll start the brainstormiung.
The implosion story is a cover up and they actually entered the hollow earth through an elaborate system of locks and dams in order to meet with Peter Viereck, who has been reigning over the sub-subterranean ape people as a tyrant since 1952. Using the mystical power of orgonism they will return to the surface and subjugate humanity to build a giant crystal pyramid from which they will fight the Posada aliens. Our Orca comrades are trying to stop them by incapacitating their agents off the coast of Gibraltar.
A NAFO sleeper agent, misdirected during movement to the Nordstream pipeline to meet up with the rest of his unit, is accidentally activated after a random series of inputs on the MadKatz controller flashed the subconscious cue to activate for the demolition mission.
Or, the second Xcom, Terror from the Deep wasn't a work of fiction but a simulator to train kids to be able to lead submariner marines to fight the unknown aliens hiding in the deep.