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I was just thinking, they could have actually made this game really different based on your paragon/renegade alignment. The paragon path would be more or less the same as now, but the renegade path would actually allow you to rejoin Cerberus and help the Illusive Man control the reapers.
Probably somewhere around the halfway point based on your paragon/renegade alignment as well as certain choices made earlier, you could change your allegiance. Some additional choices in the earlier segments of the game would help cement you towards your path could include:
-Mars Archives: Here EVA offers you a deal in secret (provided you gave the Collector base to TIM in ME2) and gives you a secret data disk. Once onboard the Normandy, you can open the disk and TIM will tell you to use this disk to erase EDI. EVA takes over the Normandy while pretending to be EDI and acts as her replacement.
-Extracting Eve mission: In the last cutscene where Shepard goes over to the almost dead Cerberus soldier, the soldier tries to give him a data disc and you can choose to take it. This will trigger a cutscene later on the Normandy where Shepard gets a direct message from TIM telling him about his plans.
-Salarian Councilor deal: The Salarian Councilor will still offer the same deal, but you get an additional choice to convince the Councillor to ally with Cerberus.
-Tuchanka: You will need to trick Wrev/Wrex, then kill Mordin to prevent him from fixing the Genophage. Eve get's secretly kidnapped by Cerberus forces while you lie to everyone that she died from the cure. If Wrex is alive, he will later confront Shepard on the Citadel (like if you lied to Wrex) about working with Cerberus and kidnapping Eve, and Shepard will kill him.
-Cerberus Attack on Citadel: Instead of the Salarian Councilor (who's now allied with Cerberus) it'll be the Turian or the Asari councilor that Kai Leng goes after. However, you get a message from Thane/Kirrae about them trying to stop Kai Leng, so your reason for that part of the mission is to kill Thane/Kirrae and help Kai Leng kill the Turian/Asari Councilor. You pretend to help Thane/Kirrae only to stab them in the back, allowing Kai Leng to kill the Councilor. At the elevator area, you tell your squadmates to stay behind and guard, while you head to the top. When you arrive, you can trick Ashley into thinking it was the other surviving Council member as the main culprit behind the attack, and get her to kill him.
-Rannoch: Everything mostly plays out like normal, except you infect Legion with a Cerberus modifed version of the Reaper upgraded code. When Legion upgrades the Geth with it, they become fully under the control of Cerberus. The Quarians are destroyed.
After this point, your teammembers finally figure out that you have been working for Cerberus this entire time. Some crew members will stay while others will leave:
EDI: If you did not replace EDI with EVA, you will need to use a Cerberus data hack to destroy EDI. Joker will leave/die if you do that. If you did replace EDI with EVA, EVA will pretend to be EDI and convince Joker to side with you and Cerberus.
Ashley: If you convinced her to become a Spectre and tricked her into killing the other councillor, you can make your other teammates think she is working with you, forcing her to join you.
Liara: If you romance her, she will join you. Otherwise, she will leave.
Javik will join you because he believes the ends justifies the means, while Vega, Garrus, and Tali will leave.
If you do not have EVA, you will get EVA2 as a replacement. Kai Leng will be a new squadmate. You will also get a new modifed Krogan clone (what capturing Eve was for).
At this point, since you are no longer undercover, all N7 missions involving Cerberus will be reversed. You will kill Alliance/Allied forces trying to take the Cerberus bases. The Citadel will have also been taken over by Cerberus with Udina in command.
-Thessia: You learn from TIM that your former squadmates are going to Thessia to find the key to the Catalyst. You basically trail them and attack them at the end, taking the VI and killing one of your former team members.
-Horizon: Your mission here is to get the DATA from Miranda's father. You kill Miranda's father but can choose to spare Miranda or kill her. She plants the bug on you either way, leading the Alliance to the Cerberus Base.
-Cerberus Base: You actually receive a distress call from TIM that the Alliance is attacking. The mission still goes the same, except this time the Alliance has already infiltrated deep into the base and you fight them to get to TIM. In TIM's observation room you fight the rest of your former teammates and kill them. Meanwhile the Alliance fleet is destroyed by Cerberus forces.
-At this point the reapers take over the Citadel and move it to Earth anyways (for harvesting purposes). Cerberus attacks the Reaper forces surrounding Earth and Shepard still has the same mission from before. However, you only need to fight your way to the end. Here instead of getting wiped out by Harbinger, TIM sacrifices most of his troops to get himself, you, and a few bodyguards safely into the Citadel. When you reach the control room it turns out one of the bodyguards that came along was Anderson in disguise. Here Anderson tries to convince you one last time to destroy the reapers. You can choose to kill him or TIM. If you choose to kill him, TIM will try to control the reapers. You can choose to kill TIM while he's attempting to control the reapers, then take over the Reapers yourself. If you kill TIM and spare Anderson, you get a choice of destroy or control the reapers. If you choose to control, you will be forced to kill Anderson anyways.
The ending basically ends with either you or TIM controlling the Reapers and dominating the galaxy.
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