Throughout Mass Effect 3, you’ll have four conversations with the Illusive Man. In these conversations, you’ll have Paragon and Intimidate interrups appear. What you choose to do in these scenes can affect the endings.
Choice: Interrupt or not
You’ll get the first conversation during the Mission Priority: Mars, the second conversation will be during the Mission Priority: Thessia, the third will be during the Mission: Priority: Cerberus Headquarters, and the final conversation will take place at the end of the game, in the Citadel. The choice you’ll have is whether you used either of the charm/intimidate options found in each conversation (some which are hidden in the investigate options) or choosing not to this.
Choice: Charm/Intimidate used
By doing all the charm/intimidate options including the interrupts in the first three conversations will give you the choice either “But you already have” or “Then you’ve failed humanity” in the last conversation on the Citadel. Choosing “But you already have” will get the Illusive Man to end his own life, whilst choosing “Then you’ve failed humanity”, will cause him to charge at you, giving you a Renegade interrupt, leading to you killing him.
Choice: Charm/Intimidate not used
By not choosing to do the interrupts, even if it’s just the one of them will cause you not to have the final choice “But you already have” or “Then you’ve failed humanity” in the last conversation. This will put Admiral Anderson at great risk, because the Illusive Man will attempt to execute him which has a direct consequence on one of the ending choices. You’ll have to perform a Renegade interrupt to stop this, and if you miss it, you’ll get second interrupt to stop him killing you too.