Warhammer 40,000: Inquisitor—Martyr was a middling action-RPG that's been tinkered with by developers NeoCore since its release, with a 2.0 update that addressed concerns with the combat and made the entire campaign playable in co-op, and now a standalone expansion.
Warhammer 40,000: Inquisitor—Prophecy adds a new playable class, a tech-adept who is the pet-summoner of the Inquisition. Only those pets are a variety of robots. The tech-adept will be playable in Martyr's campaign for those who own both, but there's also a three-part campaign in a new subsector unique to Prophecy, with new enemies too—the tyranids and eldar.
Prophecy adds more map varieties, including giant monasteries, factories, and a desert, as well as adding new items, perks, and passive skills. You can read the FAQ for more information.