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In the rule book it says "....you must then roll one dice for each model you just set up on the battlefield. For each roll of 1, a model that disembarked (your choice) is slain"

So the question is, if I have 2 different units, say a Captain and an infantry Tactical unit, do I roll dice for each unit separately and count the Captain dice result separate? or together base on how many models inside the Transport? what does the rule means by "your choice"

The rule only mentions models not units, so all you do is play the rule as it is written:

Roll a number of dice equal to the total number of models riding in the transport, then if you roll any ones you must remove that many models of your choice.

You can choose to remove your character, but you probably wouldnt right?

It makes putting your characters in transports far less dicey.

Also this should be moved to one of the rules forums.

Haaa I see, that makes more sense since it says roll for each model not each unit, another important detail i missed.

The reason I ask cause I got different answers from different places, miniwargaming said roll all dices together, facebook WH40k official said roll each unit separate, local GW store owner said roll all dices together.