According to the being in front of him, The Catalyst, Commander Maul Shepard had three choices. He could choose to destroy the Reapers and with them all synthetic life in the galaxy. He could merge his energy with that of the Crucible and create a bled of organic and synthetic DNA. Or he could choose to control the Reapers.
The choice to destroy the Reapers was tempting. If what The Catalyst said was true this choice would put an end to the Reaper threat once and for all, but he would be committing genocide. He would not only be killing the Reapers, but also the Geth and EDI. So Shepard decided not to choose to destroy the Reapers. He would not bring death upon millions.
Shepard could barely understand the second choice, synthesis. The Catalyst had not offered much of an explanation into what this choice meant, but Shepard believed he got the gist of it. If he were to run into the beam it would somehow change every living thing in the galaxy into something in-between organic and synthetic. He did not want to force this change on the whole galaxy. A change which he did not fully understand.
He had also been given the choice to control the Reapers. The Catalyst told him that he would die, but that the Reapers would obey him. This choice piqued Shepard's interest the most. He might be able to use the Reapers as a force of good in the galaxy, repair the damage they had done, protect the ones he loved. But, he was not sure. He did not know if he would be able to stay in control, if he would still be himself or become corrupted in some way. He did not even know if The Catalyst was telling the truth or if this was just some elaborate lie.
Of course he could refuse to make a choice, tell The Catalyst to go fuck itself. But, he would be condemning countless beings to death. Even as a united galaxy they lacked the strength to defeat the Reapers conventionally. Every advanced life form would be killed. Everyone living and all those not yet born. Everyone he had ever known would be killed. Anderson, Mordin, Thane, and countless others had already given their lives so that he might have a chance to end the war. Which one of his friends would be next? Joker?… Liara? No, he couldn't let that happen. He knew what he was going to choose. He would control.
He started to walk, or more accurately, hobble towards his choice. He could feel The Catalyst's "eyes" burning into his back, no doubt analyzing and picking apart his decision. Every step he took wracked his body with pain. He had been severely injured when he was struck with Harbinger's beam. It was a miracle that he could even walk. As he got closer he could make out what looked like handles with some sort of energy between them. He dropped the pistol he had been carrying and grabbed one handle then the other. Almost immediately he experienced pain more intense than anything he had ever experienced before. Even being spaced did not compare to this. The pain was so intense that he lost his grip on one of the handles. He somehow managed to get his hand back up and continue the process.
He started to think of his loved ones, the ones he was doing this for, all the while feeling his skin char and burn. He had failed Anderson. He was the one who pulled the trigger, even if the Illusive Man had made him do it. Thane had sacrificed himself to save the Salarian Counselor. If Shepard had been better Thane might not have had to die. Mordin gave his life so the Krogan could be cured of the Genophage. Kaiden, who he chose to leave behind on Virmire, and who was lost so early in the war. He had failed these people, but there were still some who were alive, Garrus, Joker, Ashley. But most of all, the love of his life, Liara. He would not, no, could not fail her!
The pain was getting worse, if that was even possible. Since the start of the war he had resigned himself to his fate. He had had a feeling that he would have to die, that he would fall protecting others. He had accepted this. He had dodged death for far too long. Gone on too many suicide missions, hell, he HAD died. He figured death would want him back.
He could feel the end. It was close. There was no more pain. He could even feel what he thought was the Reapers, apparently it had worked. He was ready to die. But… now he could see another option. With his limited control of the Reapers he did not have to die. Instead he could make a copy of himself. Shepard would live, and another Shepard would be created to control the Reapers. Suddenly he wanted to live, to see his friends again, to hold Liara. He made the choice and the pain returned, even greater than before. He felt as though his head would explode. He fell backwards, and though he could hardly see, saw a bright blue light, and then the Citadel closing.
As his world became darkness, his last thoughts were of Liara.