Prequels have the opportunity to show the secrets that are kept from the public's eyes. The Terminus Systems are the best for this as the relative lawlessness makes for interesting settings that support unknown stories, with spectres involved as their activities would be mostly kept to themselves. This way, we can have an interesting story with no major canon-breaks concerning main events. Would take place before ME2, and have the appropriate technology and social aspects of the galaxy.
For a prequel, your character gets involved in a spectre's case in the Terminus Systems, and you are forced to accompany the spectre on his/her mission and see it done. Along the way, other characters get involved as well: a merc pledges his loyalty in exchange for his life; an asari huntress is recruited to ensure the safety of Council Space; and many more. Along the way, you get more cozy with your squad, maybe take a love interest (might be the spectre), and perform life-threatening tasks to uncover a plot concerning some tech-fanatic mercs. By the time the story hits its climax, which takes place as a suicide mission planned by the spectre, the merc leader is revealed to be a puppet of the tech he so revered, before being killed by the spectre, who shows signs of indoctrination. The spectre reveals his/her plan to have you killed before the mission was done, and now deems you and your squad as disposable witnesses, and you have to fight against the spectre as the final showdown (perhaps s/he's indoctrinated, as reaper-tech is strewn across the galaxy, and if you romanced him/her, you can attempt to reason with him/her). Depending on how well your relationship is with the squad members (not exactly loyalty missions, more of simply befriending them over time), they can survive the suicide mission and the final confrontation. At the end, the spectre is dead, the reaper-tech is destroyed, and your squad made it through okay (perfect ending). There's your happy ending. A less happy ending would be your character taking a shot for your love interest, and running the risk of dying (higher squad companionship ratings increase the risk of you surviving), and then you get the happy ending of your character with your love interest, with children of some kind, and your companions as close friends. For a bit of end-credit surprises, your character is revealed to have kept a piece of reaper-tech and is shown to have almost unnoticable indoctrinated features.
Yes, it does seem similar to ME2's suicide mission, but that doesn't mean that the idea is bad of itself. Reapers have been around the whole time with caches like the above mentioned seen in random side quests in the trilogy, so why not have clueless characters exposed to a truth they don't fully understand? If this doesn't become the game plot, I'm going to write this story as fanfiction. Way too good a story in my head to forget.