Here are the consequences for each choice: If you destroy the Collector base: Ultimately, the decision is up to you, so you'll need to decide whether to destroy the base or preserve it for Cerberus.
If you go along with the idea, certain characters will disapprove because of the horrifying events that happened there. If you question the Illusive Man or his plan, certain characters will remind you of the atrocities at the base and how the victims would have died for nothing if you destroy it. Your squadmates will offer varying opinions depending on your conversation choices with the Illusive Man and who you brought along with you. He offers the suggestion that Shepard should instead use a timed radiation pulse to wipe out the Collectors while preserving the base for Cerberus.
The Illusive Man wants to use the technology in the base to help in the war against the Reapers. However, just as they are about to do this, Joker patches through an incoming message from the Illusive Man who tries to persuade Shepard that there is another alternative. After destroying the Human Reaper in the center of the base, Shepard prepares to overload the base's system to 'blow it sky high'.
