- A House United: The Virus
- Shepard and company take the Normandy down into the stormy atmosphere of the Geth Sphere. The Normandy shakes violently as the thick rain storms batter the ship. The SR2 dips downwards toward the heart of a massive thunderous storm, summoned by the geth to damage the Reaper somewhere beneath the clouds. The megastructure, according to Legion/Union, is attempting to reject the Reaper. The Old Machine is unable to use indoctrination against the geth plethora, as the Reaper's own minds are far outnumbered by the billions of individual geth units that comprise the Sphere. As such, the Reaper has decided to upload a virus that would simply kill off enough of the geth that it could indoctrinate the reduced survivors.
- The Reaper's exact location is located by the Sphere's sensitive continental surface, but EDI recommends placing tracking devices on a few places of the actual Reaper, so that the dreadnoughts in the upper atmoshpere can have better aim and not accidentally hit the continent or oceans. Shepard takes the kodiak out of the SR2, and descends into the eye of the storm in hopes of attaching tracking devices onto the Reaper.
- The kodiak cuts through the storm, struggling against the winds. Ahead looms a shadowy mountainous Reaper, blurred by rain and clouds. Massive lightning strikes, summoned by the geth, pummel the Old Machine, while the continent beneath its legs dip in and out of the ocean, attempting to shake the hostile off. The kodiak flies in close to the back of the Reaper, Shepard opens the door, and has to shoot trackers onto certain sections of it. After the last tracker is placed, the Reaper halts, and turns around to catch a glimpse of the kodiak. It is Harbinger.
- Harbinger's voice cuts through the storm, mocking Shepard. The Reaper manages to get solid footing, and prepares to blast the shuttle to pieces, but luckily the Normandy shoots Harbinger (with either rockets or the Thanix cannon, depending on ME2 variables) before it can get a shot off. Harbinger stumbles, and tries to shoot the Normandy, which ducks away.
- If the quarians resolved their conflict with the geth, then a second quarian frigate joins the fray. This frigate has Kal Reeger on board (assuming he survived ME2) who uses his own kodiak to assist Shepard in launching trackers onto Harbinger. Because his marines are not as well armed as Shepard, they retreat back aboard their frigate. Harbinger's beams slice the frigate badly, killing most of those on board, and Kal struggles to the helm to take command of the ship.
- If Kal was killed in ME2, then the quarian ship still launches kodiak marines that help Shepard emplace trackers. When the kodiak returns to the frigate, Harbinger's beams slice the ship badly killing most on board, and the ship crashes into the sea.
- If the quarians did not resolve their conflict with the geth peacefully, then they are not present for this mission.
- Harbinger attempts to take off, but a tornado causes it to slam back down onto the continent. Legion/Union or Tali/Kal says that this is their chance to kill Harbinger, but that they can't win a space engagement with it. Shepard asks Jeff to distract the Reaper with the Normandy, while he uses the kodiak to fly in close and strike at Harbinger's hamstrings. Shepard hopes that the combination of the Sphere's weather systems and a literal crippling blow could keep Harbinger stationary long enough for the dreadnoughts in orbit to lock on (to the trackers) and use orbital strikes to finish it.
- The Sphere blasts Harbinger again with lightning, and hits it with a massive tidal wave. Harbinger struggles to get a clear shot at the Normandy, which shoots it in the legs. Shepard and his squad mates use some CAIN launchers in their kodiak to target the freshly damaged legs and specific exposed points, and further damaging the Reaper's legs. Harbinger is momentarily stunned, and the orbital strikes commence, tearing into the Reaper.
- Legion/Union says that Harbinger's virus has successfully been stopped, and that they need to find a way to finish the fight. Harbinger is still active, though damaged. The kodiak flies away from the Reaper, which has started shooting orbital strikes out of the sky in an attempt to protect itself. Shepard spots a deep rent, made by the Normandy, on Harbinger's hide, and desperately suggests launching CAINs at it. Legion/Union states that they would not do enough damage, but a powerful enough smart missile piloted into the Reaper's tear might. Unfortunately, none of the combatants has any smart missiles. The geth opts instead to upload their consciousness into a geth frigate, and use it to ram Harbinger's wound, with the potential from the ship's delicate mass effect drive substituting powerful explosives.
- Legion and Kal offer to crash a geth frigate/quarian frigate into the Reaper to stop it from escaping. Legion will actually be able to “hack” its way into controlling the frigate, leaving their stationary avatar with Shepard and company aboard the kodiak. Legion will not be hesitant to die, for in such close proximity to the Geth Sphere, their personalities and memories will be archived and assimilated into the megastructure. Kal, sure that his damaged quarian frigate won't survive, offers himself as tribute for this task. Shepard must choose between sacrificing Legion or Kal to save the geth.
- If Shepard chooses to sacrifice Legion, the geth will return to Shepard the old N7 shoulder pad strapped to its arm, graciously thanking him for his service and friendship. After the frigate crashes into Harbinger's wound, the geth platform deactivates forever, and falls out of the kodiak before Shepard, entranced by the frigate's collision with Harbinger, can catch it.
- If Shepard chooses to sacrifice Kal, the marine pilots his damaged frigate into Harbinger's wound, with a final shout out to the homeland.
- If Legion died in ME2, Union carries out the collision without permission, and without hesitation.
- For a moment, Harbinger seems to have been defeated. The Reaper slumps over, and the geth use the continental shelf to slide the Reaper into the ocean. For a moment the plan seemed successful. Suddenly Harbinger rises from the waves and launches itself into the sky. The allies attempt to re-initiate their attacks, but the Reaper avoids the lightning and orbital strikes, and rockets off into the sky. Joker notes that Harbinger has escaped. The storm subsides, and Shepard and company depart.
- Larger significance:
- The significance of these events go farther than merely showcasing the geths' power, or rejection of the Reapers. It helps solidify and validate the cooperation between geth and organic peoples – who are now able to put further trust in the synthetics, at least temporarily.
- The rachni in particular are interested in relocating to the megastructure, with the queen believing that her hive mind would work well with the geth, and their histories (particularly their histories with the reapers) grant them a common understanding.