Deimos had a hold of one of the missiles that General Shepherd sent illegally. So in a what goes around comes around, Deimos is using this as leverage. Although General Shepherd is trying to cover his own ass while doing so.
The files that are Deimos were deleted, due to Deimos ordering Shepherd to do so. The CIA are kinda somewhat stuck in the middle, not knowing the full story.
141 is caught up in the mess to stop Deimos, not knowing they are walking into a trap. They originally are going to be used to track Deimos down, and get the missile as well. They are loose ends and will discover the truth soon enough, thus why Graves and Starbane are tasks to subdue or kill them.
The half of the plan Shepherd is trying to do in the middle, is frame the hive using Jäger. Marius is somewhat catching wind of it, and playing it safe for now.
Deimos:
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(Until more more is released about who Deimos is, he is a mystery character)
