Simple i'd shove the destroy solution down everyones throats, set the game 40 years after the events of ME3.
turns out there's something more dangerous then reapers in the milky way.
the exploding mass relays wiped out system after system but the explosion had another unintended consequence.
this time the threat is organic. a species long forgotten about, who we're subjugated by the leviathans who survived their AI war, though barely.
then the first cycle came, again their numbers depleted but they survived by fleeing into the space between systems, now phobic of AI's and machines in general they redeveloped their ships purely to avoid all forms of detection other then direct visual, not heat signature, no radar no emissions. they altered their genetic structure to make them more capable of survival, the opposite of the Qurans they focused on altering themselves to be highly combat capable and by living aboard organic ships had to adapt a stronger immune system, and ensured their digestive system could extract nutrients from almost any form of life. worried about numbers always in in fear a reaper would stumble upon their living ships and wipe them out they they increased their fertility rates and gestation and development cycles.
in the aftermath of the first reaper cycle which lasted far longer then they anticipated, they found their population starting to explode, They found their home worlds incapable of hosting life, hope seemed lost, for so long they were so few and now their greatest strength had become their weakness. Until a single ship found nearby system of one planet was populated with primitive life even the highest developed life forms still lived in make shift villages constructed out of local material. but the planet did not have the biosphere to sustain all the ships they could land sustain themselves setup a colony and start over, help this other lie form develop and protect itself from the machines.
But the time in such close quarters had instilled loyalty to their kind beyond which anyone could imagine, instead they informed all the ships a delegation was formed to come to a decision, But while they talked their people were starving riots had broken out, and then one day their was a mutiny aboard one of the ships, it descend toward the planet. The other ships panicked and headed for the planet they touched down and in that moment they stopped being who they were completely, in an orgy of gluttony and violence they slaughtered all life in sight devouring planets, animals and even the villagers. they stayed on the planet for a many decades some tried to regrow crops but all in vain released from confinement of living space their population grew out of control they consumed the entire biosphere transforming the planet into a lifeless husk.
and when their was nothing left to eat? they turned on one another canibalism turned to full blown warfare where the objective was not just to kill but eat your enemy.
how many generations this went on for is unknown, what is known is a profit brought together the emerging groups under the fear that machines would return.
they would return to space where they were once loyal to one another they would find a new planet which they could feed on and that is how they would live strict controls on population ensured they could survive 1000's years on "live stock" (the dregs of their society) and then lay waste to new a world.
and this went on and on each time a they stumbled upon a world rich in life they descended like a plague after they had consumed the planet their eldest generation allowed themselves to be consumed to ensure the population was once again able to live in ships, over the raids they had developed a cycle of hibernation that lasted centuries.
but the fear of the machines never left them, anytime they detected an inorganic ship they assumed it was the reapers and so they never ventured toward the mass relays they fled into FTL the moment an advance race came towards them.
and it was through this means they survived, the countless cycles never had records of them, only vague references to ships fleeing to FTL almost as soon as they were spotted, no records of showing up on any telemetry, they were dismissed as ghost stories, never venturing into regions of space populated by advanced races they clung to the barely discovered regions, they became myths that devoured entire worlds. the reapers never had a reason to seek them out, for all intents and purposes they didn't exist.
overtime however they grew bolder popping up in regions shortly after the reapers purging to hunt and scavenging, they slowly learned about mass relays and their true meaning and learned the timing of reaper cycles and they continued to rewrite themselves becoming ever more deadly quieter and faster able to overrun worlds with standing armies in matter of days. they even started to strategically target ships with organics onboard who wondered too far or missed a calculated a relay jump. But their armaments were designed to maim and wound even the few weapons their ships carried were designed to disable a ship so they could feast and thus they were never able to compete with the head races of each cycle.
until the explosion, having detected the reapers they had gone into hibernation awaiting the time when they could feast once more, but suddenly all ships were woken at once signature of mass effect relays detonating all at once, reports from scouts ships reporting........... the machines were dead............... and the citadel races defences were offline. their enemy was dead, it was time to celebrate.
Suddenly that urge they'd long forgotten about re-emerged so many planets, moons and space stations so full of life and now they were ready for the taking.................their ships headed towards citadel space.
in the aftermath of the reaper war the citadel races had rebuilt, but with the relays destroyed and with no working AI's it took decades weaponry took a back seat as even the turians focused on fixing what was lost, a make shift network of relays were slowly brought back online powered tech removed by the reapers, things were slowly getting back to normal.
even the assari had reached a point where they could once again take to the stairs.......... unfortunately for them they were the first ones hit. the ships came out of no black completely undetected. as they called for help screaming about being invaded the council worlds were paralysed, thinking the reapers had returned. by the time they realised the truth it was too late refuges from outlying colonies and ex-patriots were all that were left were of the asari. They told horror stories of ships descending to the planet engulfed in flame and when they touched down they consumed everything in sight.
the combined forces of the citadel species rearmed and went to drive these, locusts back into the black. but the effort was haphazard the new council was unwilling to wait and forces were deployed undermanned and underarmed. but it was the sheer number of Locust ships and their ability to avoid detection that saw the first offensive a disaster.
luckily for the citadel races the locust ships could not use mass relays and as such it brought them time. the batarians were the first to make a break through in detecting locust ships, and with that several victories were small victories were made at one point the allied forces drove them back. but it was all in vain the locusts seemed to adapt quickly their ships somehow got stronger. with each new offensive. in time the locusts pushed forward slowly but sure consuming worlds in a bid to slow them down, the krogan cured of the genophage sent millions of troops to the next worlds in line its unknown how many they slaughtered before they were overrun but it gained them the allies many months and when a planet was lost they detonated nuclear warheads to deprive them of food. while the turians had turned to suicide tacts developing ultra fast fighters with mass effect drives. they drove single fighters into the locust armada then detonated the cores.
but it was no use, their numbers were too many nothing seemed to stop them, they never flinched and with each battle the locusts altered their DNA and that of their ships becoming ever more invincible....... realising all was lost, the council turned to a project from the reaper war that was proposed but never used.
Thus the Ark Project began..............