What if Shepard had a little more control and sense in her mind when she was confronted by the God Child? I don't think she'd take the load of crap he gave her at the end of ME3.
So here we are; on top of the citadel, making the single most important choice in history. As Joker would say: no pressure right?
"You must make a choice," the small child I recognized back from Earth. He was just one more reminder that the Reapers were trying their damndest to control me, but I fought it and they would not finish their indoctrination on Commander Shepard.
"No," I heard myself say. I didn't have a clue what I was doing, but I knew it was right. I wasn't going to "control" the Reapers; I wouldn't be fooled like the Illusive Man. I didn't even bother entertaining the idea of combining organic and synthetic; that was the exact opposite reason I united the entire galaxy.
The obvious choice was destroying the Reapers, but that would destroy all the Mass Relays with them. Millions, billions, of lives were in Earth's sol. System and without the Mass Relays… Who knew what would happen. The entire Quarian fleet was here, they would surely die out without the Mass Relays. So no, I would not choose to do that. Instead we will fight.
"What? You cannot-"
"I can and I will!" I turned on the little boy. He had haunted my sleep for too long. Somewhere, I knew he wasn't real, but my heart and mind were blurred. I didn't know what I was capable of anymore. Dying and bleeding, I held my ground, "We will fight until the last man! Synthetics and organics have gained peace, but you refuse to see this, so we will stand together and fight!"
The child's ghost like face seemed far more befitting in my dreams instead of here. It didn't make any sense of course. "So you will let the cycle continue?"
"No," I growled at the boy. He just didn't understand did he? "I'm not going to destroy the Geth, EDI, and all our technology just to kill the Reapers. You say we can't live with synthetics, but you're wrong. The Geth and Quarians are working together just outside, an AI is helping fight the Reapers, and you choose to ignore all of this. The only synthetic left trying to fight with organics is your machines," I attacked the boy with my words, my voice growing louder until I was yelling (as much as my injured lungs would allow me to) at the top of my lungs. "So no," I stopped myself from screaming, but growled with all the ferocity of a Krogan, "I won't let the cycle continue because we will stop the Reapers here."
The see-through boy stared back at me as if I announced Santa wasn't coming to give him presents this year. I sincerely hoped his fears were confirmed upon finding out that he was behind the whole "Reapers killing all organics" situation.
"Fine. Good luck Shepard," he said darkly and all emotion was once again struck from his face. Before I knew it I was knocked out again for the umpth time that day.
When I woke up, I was found in the rubble around the Crucible, and the Reapers were losing the good fight.