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Does the order have any influence on the story? E.g. Playing the protoss missions after Hanson left the ship (because all of her missions are complete), maybe leads to a missing cut scene because she can't comment it.

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The order of the missions does not matter, there are no special cut scenes either way. The only two exceptions are first the iirc 3 missions where you have to decide which of the 2 sides you play for and second once you start the mission on the Zerg Homeworld you can't do any of the unfinished previous missions after that.

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As you say, after Hanson leaves the ship she is unable to comment on anything. The same applies to Tosh, as he will leave the ship if you choose ghosts over spectres. I cannot think of any other story affecting mission order choice.

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