Secrets: What happened

So, what happened to the Reapers, exactly?

An important part of the plot is that nobody knows for sure what happened to the Reapers. They vanished. Are they dead? Retreating? Have their completed their part of the Cycle? Are they somehow busy? Mad?

Well, only the GM can provide an answer to these questions. Here are a few options.

Option 1 – Destruction
During the Battle for Earth, the Joint Fleet managed, at a heavy cost, to land and activate the Crucible. This engine, designed and refined by countless civilizations, did its work exactly as hoped: it destroyed the Reapers. Not the Reaper troops – the Crucible wasn't designed for that – just the Reapers. The Reapers were disintegrated instantaneously, turning in flashes of energy so powerful that no recording instruments could determine for sure what happened.

But the Reapers are intelligent and ancient. Eons ago, perhaps in the very first Cycle, they had devised a contingency plan, should galactic species ever get the best of them. The Relay Virus was designed to turn these species into Reapers, over the course of years of infighting. The Cycle must continue.

Saving the galaxy
In this option, there is no single victory that can save the galaxy. The Relay Virus must be beaten by scientists and on the ground. The Reaper Troops must be beaten or negotiate.

If help comes, it may come from the Collectors. At their sunset, Protheans managed to reverse-engineer the Mass Effect Relays and build new ones. While Collectors are but a pale shadow of their genetic ancestors, Awakened Collectors are scouring the galaxy, looking for all traces of the Prothean empire, attempting to resurrect it through cloning and through the use of psyching imprints. With some help, the Collectors could find a way to deactivate the Relays and cleanse them, or even just to replace Relays one by one. If a cure is found to the Virus, the Protheans may also be able to have the Relays propagate the cure.

Help may also come from Leviathan, who first discovered the Mass Effect.

But at what cost?

Option 2 – Control (Shephard)
During the Battle for Earth, the Joint Fleet managed, at a heavy cost, to land and activate the Crucible. This engine, designed and refined by countless civilizations, did its work exactly as hoped by Cerberus: it uploaded a human mind to the Intelligence guiding the Reapers.

And Shephard-Intelligence managed to lead the Reapers away from the galaxy. But without a better understanding of the Reapers and the Intelligence, and underestimating the ability of Reaper troops to carry on without the Reapers, she failed to deactivate the troops, just as she failed to disarm the final cleanup mechanism that the Reapers always leave behind to make sure that they have not forgotten intelligent beings: the Relay Virus.

Saving the galaxy
In theory, Shephard-Intelligence could save the galaxy, if she was made aware of what happened. The hard part will be telling her: how do you talk to a god that left?

In this option, there is a single victory that can save the galaxy: entering the Citadel, from either Illos (which may be controlled by Reapers Troops, Joint Fleet or perhaps Awakened Collectors) or London (which is still controlled by Reaper Troops), then infiltrating the Crucible, and uploading the PCs to the Intelligence.

This will allow Shephard-Intelligence to deactivate both the Reaper Troops and the Relay Virus.

Option 3 – Control (The Illusive Man, with free will)
During the Battle for Earth, the Joint Fleet managed, at a heavy cost, to land and activate the Crucible. This engine, designed and refined by countless civilizations, did its work exactly as hoped by Cerberus: it uploaded a human mind to the Intelligence guiding the Reapers.

And The Illusive Man managed to lead the Reapers away from the galaxy, thus removing the immediate threat of all civilizations being extinguished within a few months. Now, the Illusive Man has some time to familiarize himself with the Reapers, test their limits, find out how to control the troops and the Reaper Virus itself. Once he is ready, the Reapers will return, as agents of a New Order. But in the meantime, the galactic species are alone in the fight.

Saving the Galaxy
Technically, the Galaxy doesn't need to be saved, as the Reapers will eventually return as saviors of Mankind. Of course, other species might not be quite as happy. In a few months, or in a few years, the galaxy will be very different: a totalitarian New Order, led by Cerberus in the name of Humanity, in which Indoctrination, Reaper troops and Reaper-level technology will ensure loyalty of all species. Fighting this New Order should be an interesting campaign. See option 4 for the kill switch that may work once to defeat the Illusive Man once the Reapers have returned.

Option 4 – Control (The Illusive Man, Indoctrinated)
During the Battle for Earth, the Joint Fleet managed, at a heavy cost, to land and activate the Crucible. This engine, designed and refined by countless civilizations, did its work exactly as hoped by Cerberus: it uploaded a human mind to the Intelligence guiding the Reapers.

And so, the Intelligence was augmented by that of a very intelligent man, who unfortunately was himself under the control of the Reapers. The Cycle will continue.

Perhaps not. The Illusive Man had planned for this contingency. He was shrewd enough to recognize the first signs of Indoctrination when they arrived, and so he had his medical staff introduce an implant in his brain, designed to release a virus based on Reaper technologies that would break the link between the Intelligence and the Reapers. Realizing that Indoctrination would get the best of him before he had a chance to upload his consciousness, he left the trigger in a hidden place, where only Commander Shephard could find it, and then had his own memories wiped.

Saving the Galaxy
While Commander Shephard is dead, the trigger still exists. The three Heads of Cerberus know about its existence. The data captured by the Alliance during the Assault on Cerberus HQ contains the name of the doctor who performed the operation, who may in turn lead to the engineers who created the virus and the trigger.

Option 5 – Symbiosis
During the Battle for Earth, the Joint Fleet managed, at a heavy cost, to land and activate the Crucible. This engine, designed and refined by countless civilizations, did something entirely unexpected: it triggered another plan devised by the Intelligence. A plan that was designed to replace the Cycle of violence and destruction by a virus.

Progressively, the virus is converting both biological species and synthetic constructs into biosynthetics. Technologically, the virus is no more complex than the process that already turns Humans into Husks, Turians into Marauders and the other species in their Reaper troop masquerade. These Biosynthetics, however, are much more sophisticated than Reaper troops. They can learn and evolve. They can reproduce and forget. They can die but they can be backed up, replicated and repaired. And they can join into larger organisms, progressively evolving towards what the Reapers consider the ultimate biosynthetic lifeform: themselves.

Saving the Galaxy
Essentially, the method will be the same as Option 1 – Destruction.

Option 7 – Don't Fear the Reapers
The Reapers have cleansed the Galaxy countless times. They have destroyed civilizations much stronger than those of the current Cycle. But, somehow, they had never met such a fierce resistance. They had never met the Thanix cannon or the Thanix missiles. During the few months of the Reaper Invasion, a dozen of Capital Ships have been destroyed. During the Battle for Earth, Harbinger itself was damaged. And the Joint Fleet managed to land the Crucible on the Catalyst, something that had never succeeded in past Cycles.

For the first time since the days of Leviathan, Harbinger is facing its own mortality. The Intelligence is facing the possibility of failure. While the Reapers are disproportionately more powerful than the Galactic Species, for the first time, they are scared. So they did something very organic: they ran away, to regroup, to repair, to plan. Behind them, they left their troops and the Relay Virus, in the hope that these will suffice to destroy the galactic civilizations. But this Cycle has become too dangerous for the Reapers themselves.

Saving the galaxy
Essentially, the method will be the same as Option 1 – Destruction. The main difference will be that, if the Galactic Species succeed, they may find eventually find themselves in negotiations with the Intelligence.