Choice: Tali vs Legion
After finishing both, Tali: Treason, and Legion: A House Divided, Joker will tell you that “Tali, just went to have a chat with Legion”, he’ll suggest that you head straight to the AI core room, which can be found in the far room in the Emergency room, within the Crew Quarters. When you get there, Tali will tell you that she caught Legion scanning her Omni-Tool, and it was about to send data about the flotilla back to the geth.
Legion won’t deny it, and instead, explains their reasoning for it. They’ll tell, that Talis fleet performed weapons tests, and were discussing plans to attack the geth, and they believed it was necessary to warn their people. Now you’ll have an important choice to make.
You’ll get a very high persuasion check, so only pick these if either of your Paragon/Renegade is fairly high. You can either charm by choosing “You’re both right” or intimidate by choosing “Knock this crap off”. Either way, you’ll be able to successfully reason with both of them, which’ll keep them both loyal to you, and if you’re in a Romance with Tali, this will not be disrupted. Whether you choose the Paragon or Renegade answer, you’ll get rewarded with 15 morality points towards the morality of your choice. Choosing this option will give you +1 reputation in Mass Effect 3.
Choice: Back off, Tali
By telling Tali to back off, she’ll become upset with you, making her disloyal to you, but it will keep Legion’s loyalty. Also, she’ll permanently end any Romance you had with her. After the scene, you can talk to her again, and choose the Paragon choice “We need Legion” or the Renegade choice “He’s not a pet” to restore her loyalty. You can only do this if your Paragon/Renegade is high enough.
Choice: Legion, stop transmitting
By telling Legion to stop transmitting, they’ll be upset, and end your loyalty with them. After the scene, talk to Legion again, and choose either the Paragon choice “You’re right, I am sorry” or the Renegade choice “I lied to her” to restore their loyalty. You can only do this if your Paragon/Renegade is high enough.