Playing through ME2 for just the second time yesterday (thanks to Bioware for fixing the horrible planet scanning), I was struck by the number of times characters mentioned dark energy in conversations, including major missions.
I'm not doubting Bioware's skill at storytelling, but it's unlikely that they'd invest the time, money and voice acting to include these references in the game without it meaning something reasonably important. Or, to put it another way, I don't think they'd throw in a red herring plotline with this amount of detail.
To be specific, these references are:
- Tali's mission on Haestrom, involving research into dark energy and the system's sun aging prematurely
- Gianna Parasini on Illium stating that there has been a sudden spike in interest in dark energy research
- Kal'Reager in Tali's loyalty mission mentioning that the cause of the weird dark energy phenomenon wasn't natural, or geth-created
To my mind, this has to have some kind of consequence for the third game. It's obviously no accident that it's coinciding with an apparent Reaper invasion.