If every time you kill a Legion member gets you bad rep with Legion how does it affect story line quests like the one at the Legion bunker and when you go to The Fort.

Don't kill everyone at Cottonwood cove and you can use a disguise if your rep is bad with Legion to get access to the fort, so basically don't kill the guy at cottonwood cove by the docks.

Shouldn't this be in the spoiler section?

Well the main reason I am asking this is because according to the wiki I need to perform some anti-legion quests to upgrade Boone. My concern is that I don't want to have to fight the whole Legion when I decide to finish the Platinum Chip decryption quest (I already started it but I left the fort)

PS How far off am I from beating the story line and will I ever need to go to the fort after this quest?

The only storyline that doesn't go to the fort is the NCR one. The other 3 you will need to go to the fort

Three out of the four storylines have you fighting against them anyway, but after you confront Benny at the Tops, Caesar forgives you all past transgressions and invotes you to the Fort.

I was shunned by the time I had to get to the Fort, and Boone was with me (who is all about killing Legionaires without my saying), so I had to tell him to stay put, and as long as I had the Mark of Caesar, the ferryman Legionaire would not attack me.

Of course, once I got over there and saw what he was doing with slaves and how he treated women...well.... Caesar's gonna be getting a dedicated Gobi .308 in the head sometime soon, I can tell ya that!