Even though John had some conflicting emotions to deal with, there was still a mission to complete. After helping Tali, John punched the coordinates for the Derelict Reaper that TIM gave him. During the journey, John still dealt with his own personal problems concerning Tali, and finally decided to tell Tali how he felt and damn the consequences. However, that would have to wait until they retrieved the Reaper IFF.
Not too much to say about this mission, other than the fact that John wanted to complete the mission ASAP because he didn’t want to end up like the former researchers. Halfway through, John(with Garrus and Tali) found most of the researchers. They all ended up on Dragon’s teeth. Tali and Garrus had a few comments about this as well. They were also surprised to see a Geth that didn’t try to kill them. In fact, it actually helped them. Once they finally destroyed the Reaper core, John went against his better judgement and brought the Geth aboard the Normandy(Tali wasn’t thrilled).
During the Mission debrief, Jacob and Miranda were having an argument about what to do with the Geth. John thought about trolling them, then thought better of it. He also decided to activate the Geth and interrogate it(maybe learn some possible weaknesses that would help the Quarians). Besides, it also helped them for some reason, and could possibly be valuable in the upcoming mission. Miranda tried to disuade John, but he would have none of it.
When that touchy subject was finished, they discussed the IFF. EDI said it would take some time to integrate it safely with the Normandy. In the meantime, John could talk to the Geth and tie up some loose ends.
After the debrief, John headed down towards the AI core and activated the Geth. Once the Geth was “resuscitated”(Not sure if that word is applicable here, but you get my point), John had a nice little chat with the Geth. During this exchange, The Geth told John that he did not face the “true Geth” when he was going after Saren. Rather, it was a splinter group known as the Heretics. “Geth build their own future. The heretics asked the Old Machines to give them the future. They are no longer part of Us.” John remained skeptical, but decided that this Geth wasn’t an immediate threat. John wanted to know what to call this Geth, and EDI thought Legion was a good possibility. Legion agreed.
After talking with the Geth christened Legion, John needed some time to think about what it said. In the meantime, he headed down towards Engineering so he could talk with Tali. While they were talking, she also sounded like she was sick. During the firefight on the Alarei, a stray bullet got passed her shields and pierced her suit. The wound got infected from carelessness, and John asked if she was going to be OK. She said she would be fine, and the conversation shifted towards what John wanted to talk about. Kelly was right, Tali felt the same way about John, and he told her he felt the same way. She was pleasantly surprised, but also embarrassed, and both agreed to continue the conversation later on.
John then headed towards his cabin so he could think about what Legion said. He didn't fully trust Legion, but decided he’d give him a chance. He noticed a datapad on the corner of his desk while he mulled things over, and picked it up. It was the note he found on Omega concerning the Mercenary groups and their possible coup attempt on Aria. John completely forgot about that, and told Joker to head towards Omega. Before he gave her the datapad, she wanted his help concerning a Krogan named Patriarch. When he met Patriarch, he told him about the Mercs. Patriarch wasn’t keen on the idea of hiding, and Shepard volunteered his services(he thought he’d humor the old man). After dealing with the mercs and telling Patriarch the good news, John headed back towards Aria. She wasn’t all that thrilled with the results, but John was able to steer her displeasure towards her batarian lackey when he gave her the datapad(John was enjoying himself for once, and he didn’t even need any alcohol). As thanks, she gave him the location of an Eclipse data cache. John then headed towards the cache and was able to secure all the crates that held intel on Eclipse(one of the few times where that rocket launcher is quite useful
)
When that was finished, Kelly told John that Legion needed to speak with him. Once he was down in the AI core, Legion told him about a virus that the Reapers created that would make all Geth agree with the Heretic’s logic(a math error? Really?). It was housed in the heretics main base of operations, and Legion wanted John’s help to deal with it. John wasn’t going to allow the Reapers to strenghten their power base, and agreed to help Legion. John brought Tali along as well(her hacking abilities would prove to be quite useful on this mission). Once aboard the base, Legion said that there was another possibility to deal with the Heretic threat. The virus could be repurposed to make the Heretics agree with the True Geth’s logic instead. John didn’t like the idea of brainwashing, and also thought that the Heretics should deal with the consequences of their actions. At the end of the mission, John told Legion to destroy the base.
Once back on the Normandy, Tali and Legion got into a “disagreement” concerning the Quarian’s possible war with the Geth. Legion hacked Tali’s omni-tool, and tried to send the data that Tali obtained from the Alarei to the rest of the Geth. John(who was still skeptical of Legion) ordered him to not send that data because doing so would only facilitate another war between both groups. Legion reluctantly complied, but told Tali that her people would answer for their actions after the Reaper war was concluded. Tali thanked Shepard, and headed back towards Engineering.
After that was settled John headed towards the lounge so he could have a couple of drinks and to blow off some steam. He thought about his last conversation with Tali, and decided to head towards Engineering himself so they could pick up where they left off. Tali waved John towards the drive core so they could have some privacy, and apologized for her earlier behavior. She told him that she was being selfish, and that she allowed her personal feelings for him to cloud her judgement. She didn’t want John to be distracted either, which could jeopardize the mission . She even said that he deserved to be with someone that could actually make him happy since she would always be stuck in her suit. John told her it was OK, and that he wanted to be with her nonetheless. Tali was thankful, and told him that she would do some research so they could make this work.