Well I do feel that the colony part sound be a very important part of the story, but I feel as though we should carry the story past that. First encounter the squad is basically overwhelmed and takes some loses (possibly npc that were also hired for the mission or maybe even a minor character controled by one of us that we don't mind losing).
After what they find at the colony the squad begins to realizes the danger posed to the whole galaxy. Kind of like how Shepard did with the collecters in ME2. They go on to try and investigate other small colonies that have been wiped out by scouting Reaper forces and in true ME fortune they get tangled up with powerful criminals, merc gangs, and of course Cerberus. Then when the main Reaper forces finally come they find themselves caught up in some of the major battles while trying to find a way to beat the enemy against all odds
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