[The Horror in the Shadows]

in The lord of the night BL book, the inquisitor is there to hunt down a tau-backed cult before they can rebel.

Necrons might have a following among the more low-tech peoples, who they might enslave/harvest later. Nercons aren't stupid, if you can get a civil war to begin then the hive is much easier to take, especially if you have traitors infilirating the enemy hidden strongholds, the traitors would just be killed last.

For nids, its there for the genestealer cults. so are limited to genestealers and maybe lictors

Cunning ork boss might make a deal with a corrupt imperial in a lust for power (see Herman Von Strab of Armageddon in
Annihilation Squad BL book)

Eldar backed rebellion might be used to avoid a imperial gerenal attacking a eldar craftworld etc.

witch/demon hunters inquistor leds the people against a corrupt lord

space marines rally the people against the horrible xenos etc.

imperial guard led the defense of the hive with locals helping best they can

the Codex lets the player come up with the fluff for the force.