The Reapers were made by the leviathans, and were used in the ancient past of the Milky Way Galaxy, primarily for conquest by the leviathan race. Still, prior to the War of Deceit (6E 2161), the aliens pledged a significant number of these machines to the Darks. The Darks chose to hand them down to their next champion. Thus, they are the Skeleton King's personal army. The Reapers were created to indoctrinate others, and use them as puppets for their own gain. Therefore, the Reapers had the ability to "indoctrinate" other life forms, by taking control of the creature's mind, and desecrating their bodies.
After the death of Veigar, the Dark Gods looked for another champion. They found such champion in the corrupted husk known as Isidor Franz, an Austro-Hungarian scientist, magician, and puppeteer who pledged service to the dark gods over 140 years prior. Finally, after Franz's full corruption was complete, he was chosen to be the new bearer of the dark banner. He accepted gladly and renamed to the Skeleton King. He was gifted with an army. This army was known as the Reapers.
The Reapers were machines created by the ancient Leviathan race, to be used for conquest and destruction. They were terrible creations of unspeakable power, the largest ones towering taller than the Burj Khalifa tower on Earth. They were given the ability to "indoctrinate", which meant to possess other life forms and corrupt their bodies. In this way, they behaved much like the Skeleton King in "puppeteering" others into doing their will. In this case, the Reaper thralls would be used as foot soldiers of the towering machines.
When the War of Deceit officially began, the Reapers attacked Earth en-masse. The forces of Earth fought hard, but after the "defeat" of Blue Team at the hands of The Skeleton King, Earth stood for only a year against the Reaper hordes. Over the course of another century of war, dubbed the "Black Century", the UNSC was obliterated, over 80% of the human race was extinct, and Earth became a Reaper world. Also, because of the actions of the Andromeda Treaty, the Sol star was eradicated, along with the surfaces of all orbiting planets, except Earth, which was protected by Reaper shielding technology.
Blue Team returned almost immediately after the "Black Century", only to find the Reapers stronger than ever, plaguing the galaxy with destruction and terror. After a hardfought war that nearly destroyed Aetherius, the Skeleton King was destroyed and the Reapers vanished.
The Reaper forces are not limited to the star ships themselves. The larger class of reapers are known as Sovereign-Class Reapers. These are designed for mass destruction, emitting indoctrination waves, and transporting smaller Reaper units. The smaller, more combat-suited reapers are known as Destroyer-Class Reapers. These Destroyers are designed for ground battle and destroying smaller targets. Reaper fighters are called Oculi, and they vaguely resemble robotic eyes with wings and wind splitters. The largest reaper, the Harbinger-Class, is the Skeleton King's personal flagship, the Prime Reaper. This Reaper towers over Earth's Burj Khalifa. The Reaper ground forces are as follows;
Husks: indoctrinated, corrupted life forms. They are individually weak, but they tend to swarm together to overwhelm and kill enemies.
Cannibals: cannibals are bloated creatures that will feed off their dead comrades for personal body armor.
Marauders: powerful, corrupted Turian marines. They each have personal shielding and a devastating Phaeston rifle.
Brutes: a Turian-Krogan hybrid. They are bulky, large beasts that tend to charge, and rely on their massive claws for combat.
Banshees: tall, deformed female Reapers that are surrounded by a strong biotic barrier, and emit psychic screams to harm and indoctrinate enemies.
Ravagers: large, bloated insect-like Reapers with bulging egg sacs that release tiny swarmers. With large side-mounted guns, they are used as heavy artillery by the Reaper ground forces.
Harvesters: massive flying beasts with incredibly powerful mouth-cannons. They have long necks and rotted wings.
Adjutants: corrupted creatures with a bloated fluid sack resting on their necks. They use this gland to power their infecting blades, to impale prey and indoctrinate them.
Reaper Pyjaks: nimble, fast scout class troops. They have a long snout-like appendage on their face, which acts as a very powerful, long range sniper rifle.
Reaper Vorcha: lightning-fast indoctrinated Vorcha combatants. These Reapers have tubes running through their body which are filled with biotic fluids, which they channel and then spit out to poison and indoctrinate targets.
Reaper Yahg: the giant, brutish Yahg that fell victim to indoctrination. They have both arms replaced with massive cannons to blow anyone and anything into oblivion.
Reaper Krogan: the brutal Krogan made zombie, they wield heavy machine guns or flamethrowers. Their body is decaying and splitting open as a result of mutation.
Reaper Volus: corrupted Volus. Rather sluggish creatures, but when angered, they will furiously charge their enemies and self-destruct, obliterating anything nearby.
Reaper Quarians: deformed Quarians that can charge their enemies, or stand at a distance and activate their auto-turrets to pick off enemies from a safe distance.