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Hi !
So, I'll soon be the Game Master of a Rogue Trader game, and I need to know: if a rogue trader, coming back from an unknown area where nobody ever came back, is suspected of being tainted , who would inspect him ? An Ordo Xenos inquisitor, looking after any xenos sign or an Ordo Hereticus inquisitor, as the Ordo Hereticus watches the traitors ?
I can't decide myself.

Whichever one got to him first... :-)

I would say both will try and get to him.

It all depends on the political situation, and the balance of power. Most inquisitors are adept politicians and rogue traders are not to be taken lightly. Sure they will both want to check it out informally or via spies but an act that might suggest an accusation might not always be the best move to make.

Inquisitors only need the flimsiest excuse to place a case under their purview.

So any Ordo is acceptable in your example. You're clear to go with whatever you want. (I think Ordo Xenos would have the strongest claim, though.)

Ok, thanks for your help, guys !

The first one to get him, and he will check both for xenos and chaos taint. Just because an inquisitor is a member of the Ordo Xenos, does not mean he does not deal with chaos heresy.
The ordos are not official organisations, they are clubs of Inquisitors with similar interests. An inquisitor who joins the Ordo Xenos is mostly interested in xenos and will specialise in that, but he still retains the knowledge and authority to deal with all other forms of heresy.
In this case, an Ordo Xenos inquisitor is most likely to notice the Rogue Trader and be interested, since they are the ones that usually deal with fringe areas beyond the Imperium's border (since that is where xenos tend to live). An Inquisitor of the Ordo Hereticus on the other hand is more likely to be focused on densely populated areas, since that is where heresy and chaos are most likely to show up.

Depends on the Inquisitor in question and the region of space that the RT visited. I'd say that most Inquisitors would not openly suspect him (they're subtle ya know ) but would probably send their agents to spy on him.

The ordos are wide organizations, there are lot of diferences between inquisitors of the same ordo. And futhermore there are Inquisitors that does not obey the rules of any Ordo.

I suggest that you could design an inquisitor character letting the ordo unknown to the players.