The shooting has stopped, but not the yelling. Legion and Tali square off. Legion wants to upload the Reaper code to the geth collective, as it enhances their processing functionality to the point of achieving true intelligence. Tali is naturally fearful of what this might mean for her people, whom the geth were able to shred when they had these enhancements. Shepard must navigate the decision.

Your first choice is to allow the upload, or to let the geth die. By choosing to upload, a second decision branch is opened: allow the upload again, stop Legion, and a Charm/Intimidate check ("Rally the fleet" / "Warn the Fleet".
If you allow the upload twice, Legion will will sacrifice itself to distribute the new programming and the upload will be finalized. The Migrant Fleet will be destroyed to the ship by the newly-enhanced geth. Tali will join her people, casting herself off a cliff; there is a Paragon interrupt, but even with it you will not be able to save her. Shepard will gain the geth as a War Asset.
If you choose to stop Legion, or choose to let the geth die at the first decision junction, Legion will attack, forcing Shepard and Tali to kill it. The quarian bombardment annihilates the geth completely. Thereafter, the Migrant Fleet joins as a War Asset, and Tali will join the Normandy crew as a teammate.
Performing the Reputation check is the most difficult, as it requires a number of factors to line up over the course of your three-game save file. If Tali and/or Legion are not present, the Charm/Intimidate options may not even be available. However, even if they are, you'll still need to have done some of the following:
Destroyed the heretic geth in Legion: A House Divided, which gains 2 "Compromise Points".
Prevented Tali's exile in Tali: Treason, which gains you 2 Compromise Points.
Brokered a peace in the Tali/Legion post-loyalty conflict, which gains you 1 Compromise Point.
Completed Rannoch: Admiral Koris, which gains you 1 Compromise Point. You can gain an additional point if you actually save Admiral Zaal'Koris vas Qwib Qwib, instead of allowing him to sacrifice himself for the sake of his crew.

You must have at least 5 Compromise Points and have 4 bars of Reputation in order to pass the Reputation Check. However, if you can, a compromise is possible. Legion continues to upload and Shepard gets the fleet to stand down, building on his/her reputation and pointing out that neither race wants war, and it is only misplaced quarian fear of reprisal that motivates the current hostility. It works: the quarians stand down. However, Legion then announces that he cannot fully upload the Reaper code without dissolving his 1183 runtimes and disseminating them throughout the geth collective. The entity known as Legion ceases to exist, but not before referring to himself as "I" for the first time, and hearing Creator-Tali tell him that yes, he does have a soul.