Version One:
"'Nowhere' was run by an old sasquatch named Lukashev. Found as a baby at 25,000 feet, he was captured and trained. His youth was spent as part of a super-naut space program along with a chupacabra and a dinosaur from the future."This version goes full Kirby and quite possible layers on the gonzo. The Time War is strange--and fought by strange combatants with stranger weapons. Lords of Creation probably has some inspiration for this version (it might even provide a system if you could figure out how to play it.).
- Brandon Graham, King City
The combatants might be as starkly good and evil as Silver Age superbeings, or they might be painted in shades of gray with the protagonists (the PCs) cheerfully unconcerned with their superiors' ultimate goals--or even possibly their identities.
Version Two:
"Just remember this: All agents defect, and all resisters sell out."Maybe there's no need to be that cynical, but this version is Philip K. Dick by way of John le Carre. The time war is more of a cold war with brief flashes of violence. The weapons are still strange; they just get used less often. Individual agents might be a bit like 007 for a bit, but ultimately they may discover they've become Number 6 and all of spacetime is the Village.
- Naked Lunch (1991)
The Agency is shadowy--and may in fact be the same as the Enemy, just at a different point on their timeline. All of this can be grim or even horrific, but it can also be played for satire (think G vs. E, and the relative amorality of Good and Evil in its cosmos).
Version Three:
Or, you could dial both of them back a bit and crash the two together. This is probably the Grant Morrison version (The Invisibles and The Filth would be good inspirations, here). Time agents are eclectic and flamboyant, but not usually Yeti's from alternate timelines. The weapons and battles are psychedelic, but the stakes can be grim, and the moral fog never dissipates--even in higher order dimensions.