I'm not familiar with the fandom but kudos to any story that has someone saying "Hey, you need something done? I'm your ninja!" :D
Generally it's a fine first draft from the look of it (bearing in mind that I don't know the fandom) but the tiny technical mistakes I found were (my suggestions in brackets):
So far, negotiations has (had) been fraught and Reeve has (had) managed to keep quiet about the power generator
I know Shinra have (has) been questionable in the past
I'm prepared to accept that Rufus may have a very valid reason for believing this splinter group present (presents) a threat to the stability and safety of Midgar Edge residents
He answered with a slight grunt as a large stone loosed (loosened) from just above him by Vincent
Despite coming into the story in the middle, I could still follow the gist of what was going on and found the dialogue and what was going on in the plot interesting enough.