From the description of the game called Natural Selection 2: 'Choose to play as a bootstrapped Marine or a beastly alien in the action-packed battle for ultimate survival. Natural Selection 2 flawlessly combines a multiplayer first-person shooter with real-time strategy elements for a game that is addictive, immersive and exciting! The tightly designed shooting mechanics combined with intricate maps create a competitive challenge for all players.' The text comes from: http://www.humblebundle.com/
I'm familiar with this game so have some context. Since the game is about marines deployed on alien planets or infested human colonies, and the fight to survive, I think the use of 'bootstrapped' is meant to confer a sense of self reliance, or self initiative. The marines are in it alone and can only rely on themselves to survive.
- Verb: To promote and develop by use of one's own initiative and work without reliance on outside help
- Adjective: Undertaken or accomplished with minimal outside help.
By these definitions, it sounds as if they're trying to say the soldier is an individual who 'does things on his own, without any outside help'.
It's an awkward construction to be sure, but given the context of it being a Marine in a video game, and it being a player character, them being 'all on their own' seems very likely.