Well, a typical 'Inquisition' would follow this format, more or less:
1. The problem is noted. Inquisitor Valerio receives a disturbing report, notices something is missing or wrong, finds a strange artifact, has an agent go missing...something that makes her start looking. No battles, but may be related to the aftermath of a battle; for example, the IG deserter was throwing lighting from his fingers when he was tracked down.
2. Reconnaissance. Valerio sends out small strike teams, gathers intelligence, and researches the extent of the problem. Battles could be fought over rescuing a friendly spy, defending a library that contains important documents, 'extracting' an enemy for interrogation or, if Valerio isn't careful, to preemptive strikes by the enemy before she learns too much.
3a. Both sides are aware of each other. The gathered information is acted upon, people start vanishing, the enemy is isolated. Battles could take the form of raiding safe houses, pursuing quarantine violators, suppressing riots, and causing/preventing sabotage.
3b Environmental factors. The Genestealers have already started a civil war, the Tzzentch cult is putting pressure on the planetary governor, the indigenous life is hostile, Valerio needs to earn some favors, some third party tries to take advantage of the situation. These events aren't directly related to the Inquisition but must be taken into account. Battles could be anything, against anybody.
4. The purge. Good potential for big battles as Valerio exterminates the enemy to the last organism; the enemy is desperate and will do what it takes to escape or take revenge.
5. Resolution. Followup to make sure the enemy is completely gone. Battles could be anything from killing off loyal but tainted Guardsmen to (if #4 went badly) Exterminatus. Possible unintended consequences from #3b. Perhaps something is found that leads Valerio to her next target?
Hope this gives you some storytelling ideas.