In the Mass Effect universe, the ultimate antagonists are the Reapers, a science-fiction take on Lovecraftian monsters. Almost every villain in the story can be traced back to the Reapers somehow, from Saren Arterius and his master plan to the Collectors abducting humans from remote colonies. And the Reapers have been around the block more than a few times.
These titanic machines have been invading the galaxy and "harvesting" all advanced organic races for almost one billion years like clockwork. Now, it's up to Commander Shepard, the first human Spectre, to unravel the mystery of these d0omsday machines and stop them. But what are they really, and how do they carry out their grim work?
When the Solution Becomes a Problem
Although Sovereign once smugly told Shepard "we have no beginning" while conversing on Virmire, the reality is that the Reapers were born from an ancient artificial intelligence, an AI that the galaxy's dominant race had created as a tool. One billion years earlier, the giant, aquatic Leviathans were on top, commanding many "thrall" races across the galaxy and cultivating them. However, those servant races built AI and robots that would inevitably revolt, usually in the form of slaughter. The Leviathans wanted to prevent that, so they devised "the Intelligence" to control the situation.
This backfired immediately; the Leviathans' AI decided that harvesting organic races and preserving them in machine form was the solution. It began with its own creators. Thus, by unknown means, most Leviathans were killed and converted into the organic machine known as Harbinger. From that point on, the newly born Reaper race continued to visit the galaxy every 50,000 years to repeat this process. If the Reapers saw organics creating AI, then it was time to harvest them to "save" them from dying at the hands of revolution-minded synthetics.
Methods & Minions
The Reapers believe that they have an important mission: to harvest all advanced organics and preserve them in Reaper form, allowing more primitive races to develop unhindered. But the galaxy is a big place with trillions of inhabitants, so the Reapers worked out a game plan to make their harvest invasions go smoothly. First, they built the mass relays so they can quickly go from one star system or cluster to another. They can also prevent other races from using them during an invasion, though this wasn't an issue in Shepard's time.
Additionally, the Reapers built the mighty Citadel, designing it so organics would always choose it as the seat of their galaxy-wide government. The Citadel contains a hidden mass relay, and when it's invasion time, the Reapers arrive in the galaxy through there. This puts them in a position to destroy all leadership figures in the Citadel, obtain census data and star maps, and take control of the mass relays.
The Reapers know where to find everyone and how to reach them, and the defending races are fragmented across the galaxy, unable to unite to fight the Reapers on a large scale. Individual star clusters and systems could be systematically attacked and wiped out. It's divide and conquer, Reaper style.
Still, the giant Reaper capital ships (Sovereign class) and the destroyers alone can't do everything. They emit a powerful indoctrination signal that slowly converts nearby organics into servants. These indoctrinated followers aren't always even aware that they're on the Reapers' side. They unwittingly sabotage their own people and expose them to the Reapers, who then gather them up in processor ships and melt them down into ooze.
Indoctrinating leadership figures who wield considerable power and authority is most effective, and after Earth fell to the Reapers, those machines began indoctrinating world leaders on all continents. Given enough time, those human leaders would see the Reapers as allies and forbid their militaries from trying to fight back.
Husks are the last major tool in the Reapers' arsenal. A given Reaper boasts a huge body, ultra-thick armor and kinetic shields, and a devastating beam weapon. But a fine comb is needed to root out and kill all advanced organics, so they make foot soldiers. These husks are cyborg zombies made from the members of all advanced (but never primitive) organics. It's efficient work; a person is killed, made into a husk that can find and kill more of its own kind, then collapse when the Reapers are done with it.
In the case of the Prothean race, their husks went on to become the Collectors, who (unusually) continued operating after the Prothean extinction cycle ended. Harbinger made good use of them to study and dissect humanity, and the Collectors started abducting humans en masse in the 2180s to build a human Reaper inside the hidden Collector base.
These husks may even be Frankenstein-style amalgamations of two or more races for boosted combat effectiveness, or have guns and mass effect manipulators in their bodies. At some point, Commander Shepard faced husks that had a Krogan's body but the head of a Turian. Banshees were mutated Asari that could teleport short distances, something normal Asari certainly couldn't do. Even the Rachni eventually became husks, known as ravagers.