During Legion’s loyalty mission in Mass Effect 2, players will be present with a choice. After fighting their way through the Geth ship, players will finally be in a position to stop the heretic Geth from completely overriding all the other Geth in the system.
They will be faced with a choice however, which is what to do with the remaining Geth. There are two basic options that the player can take, and the most important factor should be whether they are playing as Paragon or Renegade.
The Paragon option is to rewrite the heretics, neatly saving their lives in the process. The station will release a massive EMP that will reprogram them and add them to the overall Geth collective again. The problem with this is that any organics will be harmed by the pulse, and you will only have a short window of time to escape the station. The reward for this option is a large number of Paragon points.
For the Renegade options, players can choose to simply destroy the station, killing anything on board, including all the heretic Geth. This will once again lead to a brief window to escape the station, and a large sum of Renegade points as a reward.
If you rewrite the heretics and convince the Geth and Quarians to make peace in Mass Effect 3, it will increase the value of the Geth Fleet war asset.