Although the Reaper is dead, you still have not faced the most challenging part of the Priority: Rannoch mission. The geth and the quarians are still facing off in the sky above Rannoch. With the Reaper destroyed, the synthetic geth have been freed from its manipulative influence. However, the quarians have been at war with the geth for decades, and this one victory is not going to bring them together. So, you will find that somewhat of a standoff has occurred in the space above Rannoch.
Legion will suggest that you upload the Reaper code to the rest of the geth, everywhere. These upgrades would give the geth truly free will, and would make them more powerful as well. With these upgrades, the geth would be able to come to your aid against the Reapers. Obviously, this is a decision that the quarians, Tali included (if she is still alive) will not support. An upgraded geth could easily wipe out the entire quarian race, or so they say. If you want the support of the quarians, you will deny the geth their upgrades and let the quarians wipe the species out here and now.
There is only one way to gain the allegiance of both the geth and the quarians, and it is so highly specific and dependent upon your actions in the last game that many players will not be able to achieve it. First, you must have kept Tali alive at the end of Mass Effect 2. You will also have to have saved Tali from being exiled during Mass Effect 2 by completing her loyalty mission. Then, you have to have taken on Legion’s loyalty mission in Mass Effect 2. At the end of this mission, you should have killed the heretics instead of trying to gain their help. In order for this to work, Legion has to have lived through Mass Effect 2 as well, or else killing the heretics will have been pointless. Finally, you will have to have talked things out between Tali and Legion in Mass Effect 2. There was a certain point, towards the end of the game, where either Tali or Legion would lose your loyalty unless you had a high enough Paragon or Renegade rating. If you managed to keep both of their loyalties, you will be one step closer to brokering peace between the races.
In addition to these basic guidelines from Mass Effect 2, you have to have beaten the Geth Fighter Squadrons mission in this game, covered in an earlier guide. You also should have completed the mission Rannoch: Admiral Koris, again covered in an earlier guide, and at the end of this mission you should have saved Koris instead of his troops. If you meet all of these conditions, you can create a treaty between the warring races and take both fleets to battle against the Reapers. If not, it’s up to you which one to take.