This is one of the mandatory missions in chapter-3, and one that requires you to be a bit stealthy.
While you can go in guns blazing (as I did), it's best to avoid conflict, especially for your first playthrough, since there are also tetrapod MTs roaming the area, and they can easily overwhelm and kill you.
Also, this playthrough is on New Game+2, hence the end-game loadout.

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