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This mission must be completed prior to starting Priority: Rannoch, as it will not be available afterwards. It is quite easy, involving only puzzles and no actual fighting. It also passes you two Intel Terminal upgrades simply for completing it. Although you are asked to select squadmates for this mission, they do not really participate in the mission, they only talk during cut scenes.
After exiting the access point, you are notified of data clusters containing infected code which you need to disrupt to access it. Shoot your way through the first barrier showing up, then before you go any further, search the trail to your left; a small section of the orange tendrils to the left of the trail with orange data fragments floating around the solid code contains Reaper Code Fragments which you can retrieve and give to an asari looking for them. The data tendril cannot be destroyed, nor can the data fragments, however it can be interacted with (like a terminal or data pad) to obtain the code fragments. It is very easy to miss.
Proceed to disrupt the infection of the data clusters which takes the form of a large rounded object. Once you complete the task, the infection enveloping the data disappears and a historical video data will be played (on the PC you may need to hit 'V' to make the video play). Playing the video will give you the Intel for Improved Geth Resistors. A new path will be revealed which leads to the next data cluster. As before, repeat the disruption process and another video is played after you are done clearing the infection. Finally, proceed to the third data cluster, but just sit back and watch the video since this data cluster is uninfected. Once the video data ends, enter the access point revealed in front of you.
As the scene switches over to reality, a short cutscene shows one of your team members is being contacted by Admiral Raan, notifying that half of the geth fighters in pursuit stopped functioning, most likely due to the actions taken by you.
Back in the virtual world, you are informed that the Reaper code has adapted and can now self-replicate. If you attempt to disrupt the infection in front of you, it will restore itself. Thus, you need to search along the code trail and target its vulnerable point which is just above you. Disrupt the infection to continue.
If Legion was activated in Mass Effect 2, another video data depicts Shepard's first encounter with Legion. This scene will not occur if the Geth VI is present. The access point will be activated after the video ends. You will be shown with another cutscene showing the rest of the geth squadron stopped functioning when Shepard steps into the access point.
As you come out of the access point, head towards to the exit pod across of you. Once Shepard's back to reality, a dozen or so Geth Primes exit their pods as well, surrounding your squad. They do not attack, but volunteer to join you in the fight against the Reapers instead.
- A Geth Prime Platoon becomes an available war asset. It will disappear if the geth are destroyed in Priority: Rannoch.
- James will appear in the Normandy's kitchen area. Javik joins him if the Prothean has been acquired.
- Completing this mission will reset Shepard's equipped weapon to a default pistol, a side effect of the Commander's use of the geth "combat software". Be sure to check your loadout before beginning your next mission to avoid an unfortunate surprise.
- Admiral Xen starts arguing with Tali. Shepard can choose to "support" one or the other. Supporting Admiral Xen gives you the Advanced AI Relays war asset. (If you decided to complete this mission before Rannoch: Admiral Koris, this will happen after the latter mission is completed instead.)
- If Legion is around instead of Geth VI, Shepard will receive an email from the recently-liberated Geth Primes.
- At one point, Shepard asks why the quarians are shown masked in the historical footage, and Legion in turn asks how many quarians Shepard has seen unmasked. If Tali was romanced in Mass Effect 2, Shepard says he only ever saw one, to which Legion replies that Shepard's perception does not match the historical data.
- Upon viewing the hologram of Shepard and Legion's first interaction, it should be noted that Shepard is wearing the Mass Effect 3 Cerberus uniform instead of the one from Mass Effect 2.
- At the end of the mission as their servers are shutting down, if the geth VI is in the playthrough, the subtitles will still refer to it as Legion.
- As Shepard leaves the access pod and returns to reality, EDI will provide a status update to the squad. Even if EDI is part of Shepard's crew, the first piece of dialogue is spoken with radio static, as if EDI was transmitting from the Normandy. During this dialogue, EDI as she appears in the cutscene does not seem to open her mouth, or otherwise animate.