During your final visit to the Citadel during the mission [Race Against Time] you’ll have to fight Saren. After the fight, the Alliance navy will be in range of the Citadel, and you’ll have the opportunity to give Joker some order:
Choice: Save the Council or Not
During your conversation with Joker you’ll get three options, but there are functionally only to major outcomes:
- “Save the Council.”
Pretty straight-forward, and the Alliance fleet does as you command, taking some losses in order to rescue the Council. This will get you a healthy amount of Paragon points
- “Concentrate on Sovereign.” / “Let the Council die.”
Both result in the destruction of The Ascension and the demise of the Council, but saying “Let the Council die.” really makes it clear what your intentions are, and you get more Renegade points for it. “Concentrate on Sovereign.” on the other hand is more pragmatic, less malicious, and results in less Renegade points. Still cold-blooded, to be sure, but not nearly as vindictive.
This momentous decision, undermining the entire political leadership of the galaxy… has surprisingly few serious consequences. Either way, humanity will gain a seat on the Council (that’s another [choice] in its own right) and aside from the turian/salarian/asari councillors being different nondescript NPCs, there are few significant changes.
In Mass Effect 2 you’ll be able to regain your Spectre status as a show of goodwill by the Council, should you have saved them, while a new Council will be less generous, forcing you to wait until Mass Effect 3 to regain your rank. This has very little impact on Mass Effect 2 itself, surprisingly.
If you let the Council die, the Alliance forces will be superior War Assets in Mass Effect 3, while if you save them, the Alliance will be weakened, but you’ll get The Ascension as a War Asset to balance it out.