Missions arent repetitive unless you don't care about the story.
However the story is very relevant.
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Missions are very repetitive "Let me hack this" *swarm comes* "Open this door" "Fight this boss" That's how every single mission is in this game.
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This is a simplistic point of view though I have to agree. You don't have to defend something which can be destroyed by ennemies. You can't use your spaceship. But from one mission to another, objectives aren't the same. This is why missions aren't TOO repetitive.