Im sad to tell you this, but its a known complete overhaul in the story. The original script for Mass effect 3, when it was written by the same writters from mass effect 2, had the reaper existence being caused by dark energy. Their work was to prevent dark energy from consuming the galaxy, by controlling the races in mass effects technology and stop them before they could perfect the technology so much and over use the mass effect fields producing too much dark energy that colapsed suns. In the process using genetic material to create more Reapers, whie keeping the galaxy relatively safe short galactic term to go on their experiments to try to solve dark energy. Haestrom was simply one of the first sign showing the reapers were running out of time during our cycle, explaining Sovereign growing desperation and haste during the event of mass effect 1. It was also more in line with Harbinger original personnality: Your worlds will be our laboratory shepard!
Considering it was the original scrip from other writers and it was basiclly the whole reason the antagonis existed, its pretty much never gona be touched now that the game whole plot changed in mass effect 3.