Reaper

The Reapers, known by the geth as the Old Machines, are a highly advanced machine race of synthetic/organic starships. The Reapers reside in dark space, the empty, starless space between galaxies. They hibernate there, dormant for thousands of years, before they are given the signal to return. Their origins are completely unknown. The first Reaper known to have communicated with organic life, referred to by Saren Arterius as Sovereign, claimed that the Reapers have neither beginning nor end. Even their true name is a mystery; "Reapers" was a name bestowed by the Protheans, and Sovereign stated that whatever the Protheans chose to call them is irrelevant: "we simply... are."

Sovereign also reveals that the Reapers were the original creators of the Citadel and the mass relay network. These massive constructs exist so that any intelligent life in the galaxy would eventually discover them and base their technology upon them – all part of a scheme to harvest the galaxy’s sentient life in a repeating cycle of purges that has continued relentlessly over countless millennia.

Design
Sovereign, the first Reaper encountered, bore a superficial resemblance to a Reaper cuttlefish, with a bulky semi-cylindrical body, a tapering plate over the rear and a mass of metallic "tentacles" extending from its front end, in addition to six jointed legs extending from its body. When the Reaper fleet is revealed in dark space they are all shown with this basic design (however, one Reaper in the foreground shown when Harbinger awakens the fleet seems to resemble a scarab beetle) but with great diversity in tentacle number, shape and orientation, some with extended heads and others (particularly Harbinger) having multiple glowing eyes. This diversity is presumably due to the Reapers' reproduction method, in which vast numbers of a single species are harvested, melted down into a raw genetic paste, and then used to construct a "larva" that takes on the characteristics of the species from which it was created. However, as of the end of Mass Effect 2, it is unclear whether every new Reaper derived from organics will eventually take on the cuttlefish-like shape of Sovereign, Harbinger, and others like them, or if the majority of the Reaper fleet is derived from a long-extinct species of organics whose physical forms they now imitate.

Sovereign's design appears to have influenced the 'heretic' geth. This is not surprising, as these geth worship the Reapers as "gods", considering them to be the epitome of independent AI. Wherever the heretic geth become entrenched they build monuments to the Reapers resembling Sovereign's 'tentacles' around a glowing orb, and genuflect. Sovereign was apparently insulted by the adoration of such simple, base synthetics, but it did see their value as pawns and possible replacements for the flawed and organic keepers.

Indoctrination
Reapers and their technology have a strange effect on organic beings. Both Dr. Shu Qian and Edan Had'dah begin acting oddly after coming into contact with the "artifact" they found. This mental manipulation is known as indoctrination. Put simply, any organic being who is in close proximity to a Reaper for too long comes to believe the Reapers are correct in their goals and will do anything to serve them. Gradually the mind is eroded until the individual becomes a mindless slave no longer capable of independent thought. Sovereign could partly control the rate of this process as seen with Saren; in order for him to serve the Reaper efficiently, Saren needed a measure of free will. This eventually convinced him that the only way to preserve organic life was to submit to the Reapers provided they could prove themselves useful. Only beings of immense mental strength, such as asari matriarchs, can resist indoctrination, and even then, their resistance only lasts a short time and only forestalls the inevitable. Matriarch Benezia chose to die rather than risk falling under indoctrination again, and if Saren finally rebels against Sovereign, he kills himself to prevent doing any further damage to the galaxy. This indoctrination is permanent (with the single possible exception of Shiala) and is one of the most insidious weapons of the Reapers. Even more horrifying is that the indoctrination field remains active even if the Reaper is largely disabled and incapable of action. A Cerberus science team was indoctrinated by being inside a Reaper that had otherwise been floating derelict for 37 million years, its only obvious activity being mass effect field generation.

Technology
Even without their indoctrinating influence, Reapers are immensely powerful warships and their technology is devastating. Sovereign’s destructive power was unrivaled in the known galaxy. Each of the "tentacles" extending from its bow was equipped with a powerful "magnetohydrodynamic" weapon which ejects a stream of molten metal at a fraction of the speed of light which could tear through a cruiser in a single sustained burst. Its gigantic spinal-mounted gun was able to rip through the hulls of even the largest of dreadnought-class ships with ease, effortlessly penetrating their kinetic shields. Sovereign's defences included powerful shields that could block the projectiles of an entire fleet, along with an incredibly strong hull. Though they are sentient machines, the Reapers have habitable interiors that can transport a crew, either to help spread their indoctrinated slaves or to allow these slaves to tend to them, probably both. Speculation in the Codex suggests that each individual Reaper has a massive element zero core which, coupled with the likely enormous quantities of energies at its disposal, allows it to generate the staggering mass effect field needed to land on a planet.

However, the Reapers are not invincible. When the Reapers go into states of hibernation between cycles, they are vulnerable. By taking refuge in dark space, the Reapers ensure they will not be discovered by accident and destroyed while they wait for their vanguard to open the Citadel mass relay. A concentrated effort by the fleets of organic races could also destroy a Reaper even if it is at full power, and a single fleet managed to destroy Sovereign when its shields and weapons were disabled.

The Cycle of Extinction
For reasons currently unknown, the Reapers cull the intelligent races of the Milky Way galaxy, returning to dark space with the organics' technology and resources. The Reapers leave no evidence of their conquest, nor of their existence – only desolate, barren ruins of those who came before. However, based on the events of Mass Effect 2, it is possible that the Reapers use enslaved organic beings in order to create more of their own kind, as seen with the Human-Reaper.

The trap created by the Reapers was simple. A sentient species would develop FTL drive, but would still be limited in its speed. By leaving a network of relays capable of instant transport across the galaxy that led to the impressive Citadel, the Reapers ensured that it would become the center of galactic civilization. Further, Sovereign implies that the presence of the mass relays would lead the sentient species down a predetermined route with regards to weapons and armor technology (both of which are based upon element zero technology for the Citadel races). It is probable that this reduces the possibility of organic life discovering alternative, more advanced technology and progressing down a different 'path'; or, as Sovereign explains, "By using it [mass relay technology] your society develops along the paths we desire."

Another possibility is that since the Reapers harvest the resources and technology of the organic races, introduction of the Mass Effect technologies (which the Reapers themselves utilize) ensures the organic races will develop technology that will in turn be useful to the Reapers following each harvest.

Once the sentient races have established themselves on the Citadel with the aid of the keepers, an organic race either created or enslaved by the Reapers in order to maintain the Citadel’s basic functions without revealing its secrets, the vanguard sends a signal to the Citadel, instructing the keepers to activate the station’s hidden mass relay. This opens a path between the Citadel and dark space. The Reapers then flood through, killing the leaders of the assembled species before branching out and obliterating all spacefaring life around them.

Because the Reapers first enter the galaxy at the point that they have ensured will be the center of galactic politics, information and finance, they are able to cripple any resistance almost before the Citadel civilizations have any idea that they are under attack. The Citadel also gives them control of the relay network, cutting off star systems from each other and destroying communications.

The Reapers then use their control of the Citadel and its data to begin the most sinister phase of their attack. Records allow them to track down every settled planet and attack them, either stripping the worlds of resources or enslaving the populations with indoctrination and turning them into sleeper agents. The extinction events may be part of the Reaper's reproductive cycle, in which all the sentient life in the galaxy is harvested and essentially melted down into techno-organic Reaper shells based on the individual species' physical form.

Once they have harvested the galaxy, the Reapers wipe every trace of their existence from record and retreat back into dark space.

The Vanguard
The only living Reaper to be witnessed by any living intelligent being after the Protheans became extinct was designated Sovereign by the organic races (although the geth knew it by the name "Nazara"). It was a colossal dreadnought, several times the size of any known vessel – even dwarfing the massive asari flagship, Destiny Ascension. At first, it was presumed to be the flagship of the rogue Spectre agent, Saren Arterius, by those who encountered it.

Sovereign did act as transport for Saren and his geth minions – however, it was later discovered by Commander Shepard that Sovereign and its brethren were actually the masterminds behind the genocide. Saren began his search for Sovereign at the end of Mass Effect: Revelation using research stolen from Dr. Shu Qian, eventually finding the Reaper near or within the Perseus Veil.

The Prothean Counterattack
After the last cycle, which obliterated the Prothean empire, a cadre of elite Prothean scientists hidden on Ilos survived the genocide. It took them decades to realize the connection between the Reapers, the Citadel, and the keepers, but this discovery gave them the key to breaking the cycle forever. At the time, the Protheans were the only spacefaring race advanced enough to attract the attention of the Reapers, and had set about attempting to preserve the sentient races they saw evolving on other planets, including the hanar and humans.

The Protheans developed a plan to forestall the impending Reaper attack for future generations of sapient, spacefaring species. This plan hinged on the fact that the keepers have evolved, and now only respond to signals from the Citadel itself. As stated above, the Reaper vanguard signals the Citadel which in turn signals the keepers to open the mass relay, ushering in the next Reaper invasion. However, the Prothean scientists used a reverse-engineered prototype mass relay—the Conduit—travelled to the Citadel, and altered the Citadel signal. When Sovereign decided it was time to begin the cycle again, the keepers ignored the order.

This greatly complicated matters for Sovereign. In order to unleash its brethren from dark space, it would have to find a way to manually activate the relay from inside the Citadel. While Reapers are undoubtedly beings of terrible power and ferocity, a single Reaper would not be able to survive the combined might of the assembled Citadel races in a direct assault. It needed to find an agent that would lead it to the Conduit. This agent was Saren, who became capable of comprehending the vision from the Prothean Beacon. With a fleet of geth ships, the Reaper launched an all-out assault on the Citadel, nearly devastating the entire fleet.

Fortunately, Saren was stopped by Commander Shepard and company, and Sovereign was destroyed. How long this will stall the eventual return of the Reapers remains to be seen. Shepard knew the Reaper fleet, though dormant and hibernating, was still out in dark space and vowed to find some way to stop them.

The Reapers and the Collectors
After Commander Shepard defeated Saren and Sovereign, the Collectors began attacking human colonies and abducting their populations. Cerberus determined that the Reapers were behind this and planned to have Shepard thwart this latest Reaper threat to humanity. Over time, Shepard uncovered disturbing facts regarding the nature of the Reaper connection to the Collectors. Apparently, because humanity is a race of great genetic diversity and was the race who defeated Sovereign, it was enough to gather the Reapers' attention. It is revealed that the Collectors were originally Protheans who were captured by the Reapers and genetically repurposed to suit their needs.

The Collectors were working under the direct supervision of the Reaper Harbinger, who ordered the Collectors to abduct humans in the Terminus Systems. The captured humans were taken to the Collector Base and processed into organic matter to construct a new Reaper modeled on the human form. EDI speculated that this was the Reaper equivalent of reproduction. When discovered by Shepard, the incomplete Human-Reaper was composed of facsimiles of the skull, arms and ribcage of a human with its lower spine and torso still under construction. EDI concluded that tens of thousands of humans had already been processed. Shepard was able to stop the process and destroy the Human-Reaper.

With the Human-Reaper destroyed and the Collectors defeated, the Reapers lost any chance of using the Citadel mass relay to quickly return to the Milky Way Galaxy. Harbinger and the rest of the Reapers awoke from hibernation, and began the long journey towards the Milky Way, setting the stage for Mass Effect 3.

Notable Reapers

 * Derelict Reaper
 * Harbinger
 * Human-Reaper
 * Sovereign

Trivia

 * The idea of a terrifying and incomprehensible alien intelligence waiting in the depths of space is a feature of Lovecraftian horror. This similarity is emphasized by one of the recordings by the survey team aboard the derelict Reaper which spoke of how "even dead gods can dream." This is a clear homage to Cthulhu, as "In his house at R'lyeh dead Cthulhu waits dreaming."
 * The concept of a sentient space ship is much used in science fiction. In fact, it's a trope. See here.
 * From the cinematic showing the Reaper fleet at the end of Mass Effect 2, there are roughly 295 Reapers visible (as seen in this screenshot).