This is one of the best books I have ever read. The structure is unique and inspired. The story is excellent. There are individual threats but the overall plot is connected.
The book covers 180 years of eisenhorns life as an imperial Inquisitor. He has the right to go anywhere he wants in the imperuim, do anything, and has the power to command anyone he wants. As long as in his opinion, he is fighting the threats of man, be it aliens, deamons or heritics.
The book takes Eisenhorn all across the imperium, investigating cults worshiping chaos, tracking them down and fighting them. Tackling alien xenos at the far end of the galaxy. He really does go anywhere he wants, from ice worlds where the population lies dormant in stacis, to worlds full of mutant labours, rogue phsyker slave auctions, bars and brothels, hive cities and slums. The 40k universe is truly captured in all its scale.
Eisenhorn's own personal journey is even more dramatic. He wants to understand his enemy to fight chaos, but how much can he truly know and master before you become the very vile thing that he hunts?