Events and battlefronts
The Fall of Khar'shan
The Reapers made their entry into the galaxy via the Kite's Nest, home cluster of the Batarian Hegemony. The Batarians had made enemies of the various Citadel races and so had no allies to turn to as the machines stampeded through their space. The Hegemony's comm-buoy network was swiftly disabled, preventing the Batarian systems from mounting any adequate defensive measures. Ships fleeing from the Hegemony's core systems managed to spread word to the colonies that the Reapers had invaded the Batarian homeworld of Khar'shan, prompting millions of Batarians across the colonies to evacuate. However, the colonies only had so many ships to spare for each of their populations, leaving many more millions behind to wait for the Reapers' assault.
The Fall of Earth
With the Kite mass relay secured, the Reapers had easy access to many more systems. Their next primary target was the Human Systems Alliance homeworld Earth. As they advanced into Alliance territory, the Reapers easily crippled human government by destroying Arcturus Station, where the Alliance Parliament was located. When they breached the Sol System, they swiftly devastated the Lunar colonies and began landing on Earth en masse. Every major population centre was hit, industrial sectors were reduced to ashes and planetary defenses proved to be futile against the Reapers' might. Commander Shepard was in Vancouver, Canada when the invasion began but managed to escape off-world, leaving Admiral David Anderson to rally a resistance movement. The Commander was re-directed to Mars in order to find an ancient Prothean weapon that could be used to wipe out the Reapers; also, Shepard was tasked with rallying the races of the galaxy together in order to fight back against the invading machines. Meanwhile, as Shepard sought out allies and resources for this great undertaking, the Reapers began mass harvesting of Earth's population, using processor ships to cull thousands of people a day and indoctrinating world leaders to convince the populace to surrender willingly, making the harvest go faster and easier. Admiral Anderson's resistance would eventually discover the Reaper forces concentrating on London, England, constructing a device for an unknown purpose.
The Invasion of Palaven
The Reapers deployed a large force to Turian space, first striking the Turian colony world of Taetrus. The assault on Taetrus was an attempt by the Reapers to crush the impressive fighting spirit of the Turian Hierarchy; the colony was once the site of the worst terrorist attack in Turian history, in which a revolutionary dropped a starship on the capital of Vallum, wiping out over 100,000 people. To reassure the Turian people, the Hierarchy sent what they hoped would be an overwhelming force to take back the planet, but the Reapers were expecting such a tactic and decimated the fleet as soon as it emerged from the mass relay. When the Reapers moved in on the Turian homeworld of Palaven, they transmitted images of the Turian fleet's destruction to the Hierarchy via their comm-buoy network, further damaging the Turians' resolve.
As the Reapers approached Palaven, they were met with heavy resistance by the Turians' First Fleet, which sent several dreadnoughts to FTL-jump into the midst of the Reaper fleet. This tactic used the Reaper capital ships' size against them, forcing them to turn in order to get a clear shot at the Turian dreadnoughts, which successfully destroyed several of the colossal machines. The Reapers countered this tactic immediately by deploying a number of destroyers to FTL-jump straight into Palaven orbit and begin bombarding its cities and military installations. The Turians refused to be intimidated, however, and most of Palaven's civilian population is armed and ready to fight back against the invaders however they can.
As the Reapers turned their attention to Menae - Palaven's largest moon - they met heavy resistance from the moon's anti-aerospace defences and orbital fleet. Being denied a quick and easy victory, the Reapers began landing large numbers of Husks and other infantry to destroy Menae's numerous military bases one by one in a lengthy and brutal ground war. Primarch Fedorian, leader of the Turian Hierarchy, was trapped on Menae when the Reapers attacked and was killed whilst trying to return to Palaven. His successor, General Victus, had the news of the Primarch's death delivered to him by Commander Shepard, who arrived on Menae to bring the Primarch to a summit to organize a galaxy-wide resistance against the Reapers. Victus was rescued, but could not spare any of the Hierarchy's resources to retake Earth with Palaven under siege. In order to spare any ships, Victus requested that Shepard recruit the Krogan to help take the pressure off Palaven.
The Reapers gained an unexpected asset in the form of the human-survivalist group, Cerberus. Cerberus had acquired Reaper technology left over from the Collectors base at the galactic core and were studying it in order to harness the Reapers' powers of indoctrination. The indoctrination effect that the Reapers and their technology exhume is very subtle and Cerberus's leader, the Illusive Man, fell under their sway before ever realizing it. Believing he was acting in the best interests of humanity, the Illusive Man ordered several operations to interfere with Commander Shepard's efforts to unite the galaxy's races against the Reapers. He was convinced that he could harness their power of control and that doing so would advance the human race to dominate the galaxy. Of course, the Reapers had no intention of letting humanity survive in any form other than as one of their own.
The Battle of Tuchanka
As the Krogan were already being slowly killed off by the Salarians' genophage virus, the Reapers showed only marginal interest in the Krogan homeworld of Tuchanka. Cannibals and other ground units were deployed to hunt down the remaining Krogan clans and a Reaper Destroyer took position in close proximity to the Shroud facility where the genophage was dispersed into the atmosphere, repurposing the facility to further contaminate the planet's air and kill off the Krogan for good.
Depending on the actions and choices of the player, Shepard is left with the following options:-
- Aid Mordin Solus (or Padok Wiks if Mordin died in ME2) in breaching the Shroud and distributing a genophage cure into the atmosphere. Choosing this option will save the Krogan race and they will join the alliance in the final battle on Earth.
- Sabotage the operation and prevent the Krogan from being cured as a precaution against possible Krogan aggression in the future. Choosing this option will end with the Krogan deserting the alliance.
Whichever choice is made, Mordin/Padok will die and the Reaper guarding the Shroud will be defeated when Kalros, the mother of all Thresher Maws, attacks the Destroyer and buries it.
The Battle of Rannoch
The Fall of Thessia
The assault on Thessia did not go as smoothly as the Reapers' strikes against other races. While other species met the Reapers head-on, the Asari resorted to dangerous hit-and-run tactics to harass their attackers. By engaging in guerilla strategies--blast a Reaper ship, then jumping to FTL where they could not be tracked--the Asari forced the Reapers to remain on the defensive.
Unfortunately, the Reapers' greater numbers allowed them to accept certain losses, so they soon ignored the attacks against them and began orbital bombardment of Thessia. This in turn forced the Asari to defend their homeworld with a more traditional stance, facing the Reaper forces directly. As soon as the Reapers landed on Thessia, the harvesting began.
A swift and brutal slaughter of the Asari ground forces followed. Resistance from trained biotics barely slowed the attackers down. In the end, Thessia's minimal military forces, combined with unpreparedness in the face of an overwhelming enemy, resulted in the fall of the planet.
The Battle for Earth
Knowing that the organics need the Citadel to complete the Crucible superweapon, the Reapers capture the station and relocate it to orbit above Earth. Having acquired all available assets, Commander Shepard spearheads the combined galactic fleets' final assault against the Reapers. The allied fleet and Reaper fleet clash violently as organized landing parties touchdown in the United Kingdom capital of London, where the Reapers have established a Conduit - a small, short-range mass relay similar to the Protheans' Conduit on Ilos - for transporting humans for harvesting in order to build a new Reaper. As the organics make their advance, they destroy a number of Reaper destroyers using heavy weaponry, though their losses are significant. As Shepard's team make their final push for the Conduit, the lead Reaper Harbinger lands and attacks the advancing Alliance troops with a volley of particle beams, wiping out the entire squad except for Shepard and Admiral Anderson. Both Shepard and Anderson make it to the Conduit but are severely injured. When they reach the Citadel, they find that the Keepers are sorting through piles of human remains in an unknown section of the station. As Shepard and Anderson reach a central chamber, they are confronted by the indoctrinated Illusive Man, who has been cybernetically modified with Reaper tech and possesses a power that allows him to seize control of Shepard and Anderson's motor functions, paralyzing them. The Illusive Man manipulates Shepard into shooting Anderson in the gut and gloats over his imminent triumph, but still doesn't take control of the Crucible in order to take control of the Reapers. Shepard manages to regain control in order to kill the Illusive Man, and with both him and Anderson dead, Shepard is alone. The commander activates a console in the room that opens the Citadel's arms and allows the Crucible to dock, but nothing more happens until Shepard is carried up to another chamber where he meets the holographic avatar of an AI. This AI is The Catalyst; it is both the key component needed to fire the Crucible and, more shockingly, it is the guiding intelligence behind the Reapers.
Outcome of the war
When Shepard reaches the Catalyst chamber, the commander is faced with a choice that, for better or worse, will bring an end to the Reapers' cycle of genocide. There are four outcomes for the game player to choose from.
Shepard follows the original plan of destroying the Reapers, using the Crucible to unleash a wave of energy across the galaxy via the mass relay network. The energy overloads every Reaper construct throughout the Milky Way, causing them all to violently detonate. The wave affects not only the Reapers but all synthetics, including the Geth, and as they all explode a great deal of additional damage is inflicted across several planets. However, the worlds can be salvaged and organics have no need to fear the Reapers ever again. Shepard triggers this outcome by shooting a vital power circuit in the Catalyst chamber, causing it to explode.
Shepard comes to the realisation that the Illusive Man was right: it is possible to control the Reapers. The Illusive Man had already been indoctrinated and so could not take control himself, but Shepard has the option of doing so. Consequently, however, Shepard sacrifices everything that he is to make this option possible: his body is destroyed and his mind becomes the new guiding intelligence behind the Reapers, essentially making him into the new Catalyst and able to determine a new solution for the machines to strive for. If this function is activated, Shepard uses the Reapers to rebuild everything that was destroyed in the war and to protect the galaxy's races from whatever threats they may face.
Synthesis can be considered the 'ideal' outcome as both organics and synthetics are allowed to co-exist. By adding his own essence to the Crucible, Shepard can trigger a galaxy-wide fusion between organic and synthetic life, allowing organics to achieve technological perfection and synthetics a clear understanding of organic mentality and evolution. If the Synthesis is triggered, Shepard will die, but the organic and synthetic races will cease their conflicts and work together toward a mutual accord. The Reapers themselves will retain their vast knowledge and intelligence but gain a new insight and understanding of organics; they cease their harvesting of organics and aid them in rebuilding everything that was destroyed.
Shepard is unable to make the difficult choices at this crucial point and rejects all the options offered by the Catalyst. If Shepard rejects all three of the resolutions offered, the cycle continues and Shepard watches as the Reapers obliterate his home planet and all the people and resources that he worked so hard to bring together. However, even if Shepard's attempts to end the cycle failed, the possibility remains that the advanced races of the next cycle will bring an end to the Reapers based on information left behind by both Shepard and Liara T'Soni in time capsules that have been seeded on various planets. No matter which outcome is chosen, Shepard's name will be remembered by future generations.