If you chose to complete Legion’s (or the Geth VI’s) side mission as opposed to or in addition to the Admirals’ missions, you will have to go to Rannoch and infiltrate the geth server by physically placing yourself inside of it. Legion will ask if you trust him. Respond either yes or no, and plunge into the geth computer. You will end up in a strange, neon world of cubes that represent the inside of the geth server. The Reaper codes that have been controlling the geth will be represented by glowing orange trails that tear through the landscape. They will often appear in front of you to block your path. Shoot the orange trails to open up the path ahead of you.
This section is relatively linear, so just follow the blue path around, shooting the orange code fragments as they move to block your path off. Sometimes, you will come upon blinking blue squares. In this case, you just have to step on the squares to extend the path further. When you reach the end of the path, you will be at the server terminal. Walk into the terminal and you will be teleported to the next section of the area. Legion’s communications will begin to fade as you enter the next area. Keep moving along the linear path shooting the bad code. You will come to a group of code that is completely encrusted in orange, malicious data. Shoot it all off to free the server. A video will play showing the creation of the first geth. Keep moving forward, shooting the malicious data as you move on.
Circle around the middle of the next area and shoot off the brightly glowing sections of code to free the next data cluster as well. You will again see more holographics images of geth. You will meet Legion here as well. Watch as the geth learn sentience and begin to attack their creators. Walk forward and continue to the next area. As you proceed, the Normandy crew will begin to take a beating. They will urge you to hurry. At this next junction, you will have to destroy the brightest spots of the code before shooting the parts that actually block your path. Otherwise, the code will begin to repair itself. You will reach another cluster of malicious code soon enough. Follow the path to the left and look at the wall. Two sections of the wall will be missing, and will have strands of code protruding from them. Shoot the code, then turn around and destroy the first cluster. The second cluster will require you to destroy two more weaker sections first.
After you free the next data cluster, you will see another video of the geth interacting with the quarians. Follow the path around to find one last section that you must liberate. Destroying the Reaper code around it will reveal the outcome of the Morning War between the quarians and the geth. Completing this section will cause the geth fighters around the Normandy to shut down. You will also find that Legion has programmed a group of geth to help you fight the Reapers. Accept his help to gain a powerful new war asset.