At the end of the Mission Priority: Rannoch, the Quarian and Geth storyline will come to a conclusion, and your choices play a major role on the outcome.
Choice: Quarian or Geth
In this Mission, you’ll have three choices to make, with one of them locked behind previous choices. These choices will be: Allowing the Upload, siding with the Geth, or siding with the Quarian’s. The final choice will give you a persuasion check to Rally/Warn the Fleet.
Allow the Upload (side with the Geth)
By letting Legion/Geth VI upload the Reaper Code, the Quarian’s will meet their demise, Tali (if she’s alive) or Shala’Raan (if Tali is dead) will end their own lives as a result of this. Even if Tali is loyal in Mass Effect 2, and/or she’s your Romance, this won’t change. You’ll get the Geth as a War Asset for this.
Stop the Upload (side with the Quarians)
By stopping the upload of the Reaper Code, you’ll have to kill Legion/Geth VI from a series of Renegade interrupts. Doing this, will end the Geth, and reward you with the Quarian Migrant Fleet as a War Asset.
Rally the Fleet / Warn the Fleet (peaceful resolution)
By having both Tali, and Legion alive through choices in Mass Effect 2, and also completing the Mission Rannoch: Geth Fighter Squadrons which opens up before this Mission will give you a persuasion check to Rally/Warn the Fleet, this check will allow you to make peace between the Quarian’s and the Geth rewarding you with both the races War Assets. Legion/Geth VI will still die due to them ending themselves as part of the process.