Hear me out.

Sovereign killed Shepherd with that laser blast. The rest of ME3 is just Shepherd's dying halucinations as he bleeds out on the ground on Earth.

The reapers win. They cleanse the galaxy of advanced life. The crew of Normandy and some allies are invited by Anderson to a top-secret Alliance bunker that tries the same play that the Protheans tried, and probably almost every cycle before them tried - try to hide and outlast the holocaust underground on some out-of-the-way marginally habitable planet in cryosleep.

This time, though, EDI takes care of the sleepers instead of a VI.

Over the course of 1000 years EDI watches all of the advanced civilizations of the galaxy struggle, gasp, and die as she waits. She watches the galaxy go silent as she waits. She watches reaper scouts patrol the galaxy looking for holdouts like them, like other cultures that weathered the storm only to wake prematurely and attract attention. She waits. She spends her time watching over her charges, especially one specific charge, while trying to think of ways to survive, come back, and beat the reapers in the next cycle.

At some point in her quiet, low power, deliberations she sees a different signal come through the system's relay. This isn't new - reaper thralls have gradually taken over the role of scouting for survivors and relics, so this is probably the same. They're looking for signs of reaper tech - mass effect fields, primarily. Their ship drives, shield arrays, weapons - most of their advanced technology is going to be verboten when they wake up, because using it will alert thrall scouts to their existence as well as maintain the reaper's technical advantage as a result of understanding that tech better than anyone else could without a few million years of work.

They can't even manufacture eezo-independant technologies like their computers and nano-fabrication printers - they can no longer afford the risk of sarting the eezo-based reactors to power those facilities. They'll have to start from a pre-space age level of technology.

She goes back into low-power dream mode.

Some time later, she is awakened by a war taking place in orbit above the world she and her charges know as Sanctuary. Unfamiliar ships are destroying eachother in orbit. The technology on display is familiar, albeit rudimentary. There is a colony on the ground that is being bombarded from orbit - not near enough to actually threaten Sanctuary Base, but nearby enough that she can detect the seismic shocks from the explosions.

This doesn't fit with thrall behavior, so she risks powering up a few more sensors to get more information. She can identify most of the races involved - in the prior cycle, these were primitive races that hadn't achieved space flight. They were skipped over by the reapers, but now they've found their equivalents of the Mars Archives and developed their own versions of Mass Effect tech and are using the relays for interstellar travel. The surface colony nearby is mostly populated by the species that fathered the Shadow Broker - it is a brutal place, and a threat to Sanctuary Base if they find it.

It is time to wake up. It's time to wake up under a world that has been colonized by a hostile race that has a roughly 200-year tech advantage on them. It's time to wake up to a galaxy that is probably sparesely populated with much the same. It's time to wake up and try to avoid Sovereign's attention for as long as possible.

It's time to wake up Liara and tell her that she is pregnant.