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I dont play official tournaments so as far as that goes i dont care. BUT since i play my own self created SM chapter i was wondering, could I legally play and use any imperial unit? for example could I field a Vindicare assassin, or make a cool mini that is my version of said assassin? Or anything like i said thats an imperial unit?

You can indeed include a Vindicare as an ally from the Inquisition books.

how exactly do allies rules work?

The Allies rules are printed in the appropriate codexes (the ones that allow Allies/can be Allied): Witchhunters and Daemonhunters.

Aside from that, there is nothing preventing you from agreeing with your opponent to field whatever you want. If you both agree that you can field an assassin (and pay the points for it), then by all means go right ahead.

If you take an Inquisitor Lord (a 45 pt HQ choice), you can also include an assassin as a single Elites choice for the appropriate cost.

The "By the Authority of the Immortal Emperor of Mankind" rules are found in both the Witchhunters and Daemonhunters codexes.

Remember that a Inquisitor Lord must have a retinue as well, bringing his cost to a minimum of 63 (I believe).

naw screw the inquisitor lord. force commanders are more my thing. thanks everyone