Karpyshyn describes the early storyline as "something that wasn't super fleshed out," with a story arc that revolves around the spread of Dark Energy. This plotline is actually hinted at by a number of characters in Mass Effect 2 but never became a focal point for the story.
"Dark Energy was something that only organics could access because of various techno-science magic reasons we hadn't decided on yet," he said to VGS in an interview transcribed by Eurogamer. "Maybe using this Dark Energy was having a ripple effect on the space-time continuum."
"Maybe the Reapers kept wiping out organic life because organics keep evolving to the state where they would use biotics and dark energy and that caused an entropic effect that would hasten the end of the universe. Being immortal beings, that's something they wouldn't want to see.
"Then we thought, let's take it to the next level. Maybe the Reapers are looking at a way to stop this. Maybe there's an inevitable descent into the opposite of the Big Bang (the Big Crunch) and the Reapers realise that the only way they can stop it is by using biotics, but since they can't use biotics they have to keep rebuilding society - as they try and find the perfect group to use biotics for this purpose. The asari were close but they weren't quite right, the Protheans were close as well.
'We ended up going in a different direction.'
"Again it's very vague and not fleshed out, it was something we considered but we ended up going in a different direction."
Some fans of the series used this narrative as an example of a better solution to the series' eventual ending. Karpyshyn left the Mass Effect team before the end of Mass Effect 2 and was soon replaced by Mac Walters who would go on to lead the writing team behind Mass Effect 3. But Karpyshyn states fans would have likely been disappointed in the ending he suggested as well.
"I find it funny that fans end up hearing a couple things they like about it and in their minds they add in all the details they specifically want," he explained. "It's like vapourware; Vapourware is always perfect, anytime someone talks about the new greatest game. It's perfect until it comes out. I'm a little weary about going into too much detail because, whatever we came up with, it probably wouldn't be what people want it to be."
Karpyshyn also discusses a number of ideas that never reared their head, including one where series protagonist Shepard turns out to be an alien.
"Some of the ideas were a little bit wacky and a little bit crazy. At one point we thought that maybe Shepard could be an alien but didn't know it. But we then thought that might be a little too close to [Knights of the Old Republic character] Revan."
You can listen to the full interview here.