Operation Cleanup
From FABT
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 Geth trooper platforms in support of a Armature-class tank during their failed raid on Feros.
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20 July 2183 CE - 1 October 2185 CE | ||||||||||||||||
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Across the Attican Traverse and Terminus Systems / Milky Way Galaxy | ||||||||||||||||
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Heretics cease hostilities
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Haratar Station is destroyed and the geth lose control of the Sea of Storms system | ||||||||||||||||
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- "Not that you can ever discount them, but we haven't had any serious casualties in months. A civilian ship will spot an enclave and we'll send a squad to clear them out. They're not quite the boogeymen they used to be."
- — Councilor Anderson updating Commander Shepard on Operation Cleanup upon their return in 2185 CE.
Operation Cleanup, also known as the Post-war Heretic conflict, was the designation given for the Alliance military operation to mop up the remaining geth heretic forces still outside the Perseus Veil following their decisive defeat at the Battle of the Citadel and the end of the Eden Prime War. With Saren Arterius dead, their god-leader Sovereign destroyed and their main fleet utterly obliterated, the geth heretics were left in a severely weakened state, lacking unifying leadership and their forces splintered and scattered across the galaxy: with the Reaper invasion stopped and no leader to coordinate them, the geth heretics were dismissed as a real threat by both the Council and the Alliance, and the Eden Prime War was considered officially over: despite this, the geth heretics still posed a problem, having not retreated back behind the Veil and refusing to surrender. As such, per Steven Hackett's recommendation and Joseph H. Garrong's approval, the Alliance immediately began post-war operations to locate remaining pockets of geth forces and begin neutralizing them, one by one: this operation posed its own problems, as the geth heretics largely went to ground after the Battle of the Citadel, remaining isolated and hidden, forcing the Alliance to dedicate intelligence resources to finding these holdouts before they could be dealt with. This was made harder by the Council's lack of commitment to the same end, largely viewing the geth heretics as a purely human problem to be dealt with, and that any direct threat to Council space the geth once posed had been neutralized, and thus no further involvement on their part was required. Deprived of STG resources and turian military power to back them up, the Alliance was forced to go it alone, drawing out the mop-up process by what some estimates suggested would be years.
Frustrated by Commander Shepard's continued insistence of a greater Reaper threat, believing the threat had died with Sovereign, the Council assigned the human spectre to assist the Alliance in the geth cleanup operations, the only resources the Council would dedicate to the Alliance's efforts and mostly done in an effort to keep Shepard busier dealing with the geth than pushing for wide-scale preparation for an enemy they didn't believe existed. Utilizing the Normandy Squad's expertise in dealing with geth, the Alliance was able to chalk up some early wins, striking several major geth holdouts in the Attican Traverse. First returning to Virmire to ensure no further geth forces remained on the planet, Shepard then landed on Ilos, mopping up a significant geth force that had been left behind by Saren in his rush to get to the Citadel and had been largely ignored by the Normandy in their desperate pursuit. After Ilos, the Normandy briefly linked up with her sister ship Stalingrad to observe the movement of a geth fleet, reporting the sighting and their observations to NAVCOM before participating in a bombing run on a geth stronghold on Gei Hinnom. The Normandy would then be reassigned to the Terminus Systems, where the Alliance needed a stealth ship to destroy geth heretics holed up there, not wanting to risk sending forces officially out of risk of provoking the Terminus. The Normandy destroyed a geth facility on Volturno in the Ismar Frontier before having to split up the team to recon two reported geth sightings, one on Anhur in the Eagle Nebula and another on Klendagon in the Hawking Eta cluster, with Kaidan Alenko in command of Garrus and Liara T'Soni as they investigated Klendagon while Shepard and Tali'Zorah stayed behind on Anhur for a week to reconnoiter and verify the Anhur sighting: while the Klendagon mission was successful, no geth were confirmed on Anhur, and the only combat was due to a week-long battle with a turian mercenary named Grevel and the local batarian faction, with the Normandy picking up an injured Shepard and Tali afterwards. Tragically, only a couple days after the Anhur-Klendagon missions, the Normandy, whilst investigating the sighting of a geth ship over Alchera, was ambushed and destroyed by a then-unidentified ship, resulting in Shepard's death and that of much of the crew. The Normandy Squad was broken up not long after, going their separate ways and depriving the Alliance of their most effective cleanup team. In just a month, the Normandy Squad would rack up more geth clear outs than any other special forces or marine squad in the entire Alliance military, and it was a record that would be hard to beat in the coming years.
Operation Cleanup would drag on for two years following the Eden Prime War: by the time Shepard was resurrected by Cerberus and made his surprising return in 2185 CE, it still had not concluded. One by one, pockets of geth heretics were mopped up, their numbers dwindling as time went on, but the Alliance was still no closer to fully destroying their enemy, who had the resources to continue building new platforms and continue their struggle. Growing bolder, the geth heretics began launching raids and retaliatory strikes against Alliance assets and civilian populations in order to strike fear into their enemy. This included terrorist attacks, as was the case with the Broken Arrow Incident in March 2185 CE, where the human freighter Broken Arrow had been transporting munitions and supplies to Jonus when it was hijacked by geth heretic forces and placed on a collision course for the colony, intended to maximize civilian casualties: this was stopped by the intervention of the Stalingrad deploying a Blue Falcon squad, who then neutralized the geth boarders and reassumed control of the ship, avoiding catastrophe: two weeks later, the same team was deployed to clear out a geth stronghold on Elatha, where it acquired intel of a planned strike on Hephaestus Station, headquarters of the Andromeda Initiative, using a geth heretic cruiser that they then proceeded to stop by boarding the cruiser, overloading its reactor and escaping before it exploded. Earlier, in January 2185 CE, a geth heavy frigate, wanted by the Alliance for over a year for its preying on shipping lanes and raids on supply ships, was finally caught and ambushed near Styx Theta by a dedicated Alliance task force consisting of destroyers Belfast, Scapa Flow and Kiev and the two light frigates Verdun and Gallipoli. The frigate was severely damaged in the engagement and forced to make a blind FTL jump to escape, arriving over Aite where it was finished off by its ground-based GARDIANs, with the frigate crashing down to the surface and its wreck site later claimed by Cerberus. Despite these victories however, the geth heretics were no closer to being wiped out, and with their new headquarters of Haratar Station still undiscovered (hidden in the Sea of Storms), the Alliance lacked the capability to strike the heretics a cutting blow. As the years went on, the Alliance largely stood down the majority of its forces from the operation, relying on civilian ships to spot enclaves so that teams could be sent to clear them out. Regardless of the Alliance's inability to fully crush the geth heretics, the heretics were effectively neutered as a threat, and their continued persistence ultimately only irritated civilization rather than representing a focused threat to its existence. They were no longer the "boogeymen" they used to be, as Councilor Anderson would coin it.
The outcome that would ultimately end the heretic threat and bring an abrupt end to Operation Cleanup didn't come from military victory, but as the result of the geth themselves taking action to end it. Having allowed the geth heretics to leave in the first place, respecting their choice to side with Sovereign, the Orthodox geth finally realized the heretics were no longer a danger to just organic civilization, but to the geth as well, as their continued aggression would only result in an eventual continuance of hostilities, and an inevitable invasion of the Perseus Veil, and this made the heretics their enemy. Developing a virus that would purge the heretics' runtimes galaxy-wide, wiping them out in one fell swoop, the geth made plans to launch an attack on Haratar Station, but decided against it when the platform Legion made contact with Commander Shepard, who agreed to help the platform upload the virus instead. Halfway through the raid, the geth discovered they could instead re-purpose the virus to reprogram the heretics, wiping them of their pro-Reaper beliefs and causing them to rejoin the Orthodox geth. Shepard sided with this option, and the resulting pulse impacted every heretic across the galaxy, reprogramming them and causing them to accept the Orthodox geth's ideology. Within days, the heretics ceased to exist as a separate faction, with all remaining geth platforms beyond the Veil, with the exception of Legion, returning to the Perseus Veil to rejoin their people. This brought an unofficial end to cleanup operations as they were now rendered redundant, but Operation Cleanup wasn't considered officially completed until late 2185 CE when Shepard made his report to Alliance brass regarding the geth schism and the elimination of the heretic threat.