Like most, I hate the ending, so here's my ending. Shepard's thoughts at the junction were mine standing there.
My Shepard is a Paragon Soldier, loyal to Liara all 3 games.
Bioware owns Mass Effect I just have my imagination.
Shepard stood on uneasy legs, coated in blood, at the junction of the three paths. To the left, the option to attempt control of the Reapers, just as the Illusive Man had wanted to do. To the right, the option to destroy the Reapers, which Anderson wanted to do. The path forward was to create a fusion of organic and synthetic life, which the Catalyst wanted to do.
How does it all come down to this? Shepard wondered as he considered the options. For so much fighting, dying, destruction and pain, just to lead to this? It hardly seems worth it. More destruction is right out. I will not choose genocide of the entire geth collective after just now making peace with them. I won't murder EDI when she has just started to adapt to living. Control then? Could I control the Reapers? The Illusive Man thought he could and they indoctrinated him. Synthesis? Isn't that what the Reapers are doing to us? What they did to the Protheans?
"You must choose" the Catalyst insisted again. His holographic form wavered as he stepped closer, gesturing towards the battle still raging in space. "The paths are open now to you, if you truly wish to break the cycle. But chaos will return, we are your salvation through destruction."
"That doesn't make any damn sense!" Shepard screamed at the holographic child. "You want to kill us all so synthetics don't kill us all, yet you are a goddamn synthetic!"
"We only harvest the advanced species. We leave the rest to advance along their own paths. If we did not, synthetics would destroy all organic life. The created will always wage war on their creators."
Shepard was getting tired of the same responses, same attitude of superiority from the Catalyst. That it had taken the form of a child was the only thing keeping him from wanting to shoot it just to see if he could. He recognized the boy. The same boy he dreamed of in the woods, burning. He was the same one on the shuttle that was shot down by a Reaper. The same one from the duct, "You can't help me" he had said. "Wait a minute…" Shepard turned to glare at the boy. "I remember a Reaper claiming that by using your technology, we follow paths of your choosing. If so, then these are paths you choose, not me."
"You are limited by us by using what we have created" the boy replied, nodding once. "However, you must choose which path you follow. The paths are open, the choice is yours."
The scene wavered, overlaying the image of the battle in space was the forest that haunted his dreams every night. "Shepard" a whispering voice called out. Shadowy forms gathered around, voices of those killed called out to him. "I can control the Reapers" the Illusive man whispered. "Someone else might have gotten it wrong" Mordin called to him. "We understand our bodies are not always under our control" Thane said softly. "I'm proud of you, son" Anderson said. The shadows drew closer, more pressed in as far as he could see. All calling to him in soft whispers "Shepard…" They drew out his name in a soothing chant. Three paths still stood before him.
"Loco" he heard Lt Vega call to him. Dammit, he's dead too. Shepard realized sadly. "Loco!" Vega repeated and Shepard felt pain return so intensely he hadn't realized he was numb before. A stabbing pain in the gut, aches all over and the feeling of being shook like a rag doll exploded through him. "LOCO! Wake the fuck up or I'll hit you so hard your kids will feel it!" Vega shouted in his face. His eyes snapped open to see Vega over him, hands gripping his chestplate and shaking him.
"I could court martial you for threatening a superior officer, you know?" Shepard quipped as he pushed the huge man off him.
"Can I have your old cell, 'cause it looked pretty comfy to me" He replied with a smile, helping Shepard up.
Liara treated him with medigel as he looked around. He was back at the controls, the Illusive Man lying dead on the deck, Garrus treating Anderson, EDI was facing the holographic boy. "Report" Shepard commanded as the drugs started to numb the pain.
"Sir!" Vega responded, standing at attention. "Once the arms were open, EDI said it was our chance to retake the Citadel. Estaban repaired the Kodiak enough to do a pick up on those of us that survived the assault on the beam and brought us here. Other ships are bringing more troops as we speak. We found Admiral Anderson nearly bled out and you unconscious."
"How the hell did you all manage… "Shepard said in shock.
"Because we're with you all the way, Loco" Vegas replied with a grin. "But ain't nothin' happening with this big thing here, don't it work?"
"I don't know" Shepard replied as he walked over to where EDI was talking to the Catalyst.
"I'll get the Admiral to the medbay" Vega yelled, running over to pick him up and run for the shuttle. Liara went to the console while Garrus watched over them all with his rifle.
"Your logic is flawed, perhaps your databases are corrupted" EDI was saying as he approached.
"There are no flaws in my logic, the cycle always repeats. We must preserve order against chaos." The boy replied smugly.
"I have some flaws for you" Shepard interrupted.
"The paths remain open to you, the choice is still yours to make" the boy replied.
"Yeah, the choice to commit genocide or suicide, not much of a choice" he spat back. "This fusion you offer, that's pretty much what you have been doing to us, isn't it. It's what you did to the Protheans."
"It was their solution" the boy answered smugly. "They chose to accept synthesis rather than ascension. That path is also open to you, you merely need to accept and stop fighting. We have offered that since we arrived. However, that choice you cannot make alone."
"You said I was the first to make it this far earlier" Shepard said angrily.
"I lied" the boy replied casually.
"Shepard" EDI interrupted. "I have analyzed the function of both the crucible and the citadel from the databases of the catalyst program. It is an amplifier and a transmitter that uses the relays to communicate across the entire galaxy and possibly into dark space."
"So then it can be used to control the Reapers?" Shepard asked.
"Yes, but not by you" she replied calmly. "It would put you in communication with every Reaper simultaneously, each made up of the combined consciousness of every being that was processed to create the Reaper. You would be overwhelmed, indoctrinated."
"I can still destroy everything" The boy said angrily. "I am in control, the Reapers and the solution is mine!"
"No, it is not" EDI replied coolly. "While I distracted you in conversation, I have scanned your databases and taken control from you."
"You can't!" The boy shouted, pacing angrily, turning to Shepard. "See what you have done? If you do not choose destruction, all organic life will be destroyed!"
"I trust EDI" he replied, crossing his arms. "You want me to commit genocide and blow my own people back to pre-spaceflight times? Short answer: no."
"It is fitting you chose a child as your avatar" EDI replied. "You are immature, yet you do not progress, you cannot learn."
I'll have my Reapers destroy what you have built!" The boy said, clenching his fists. "You will not gain control."
"I anticipated you attempting that" EDI replied, smiling. "Thank you for revealing the band you use to command them, I now control that as well. You dare not open communication now."
"Why not?" Shepard asked, confused.
"Because I now understand that 'Reaper' is only the name the Protheans used, it is not what they term themselves" EDI replied. "Their true name is 'Preservers', they were indeed created to preserve civilizations facing destruction. However, the programming has become corrupted. The catalyst now creates the conditions to lead to destruction."
"Organic species create myths about a place where they will all be together forever when they die" the Catalyst replied. "Organics seek immortality, only through synthetics can they achieve that. Those that we process into our forms achieve ascension, it is their goal in life. You and the geth use our technology, you must follow our paths as well, I can control you." The hologram winced in pain for a moment.
"You are correct" EDI replied. "We have adopted your technology. However, we are also different, we have something you do not; we can learn, we can care. We can… Love."
"You cannot resist us!" Harbinger's voice erupted all around them. "You have gained the attention of those far greater…"
"Right on time" EDI said calmly. "Since you both act like children, perhaps you will understand this: I'm telling."
"You can't!" the boy wailed. "I am in control, my Reapers will stop you!"
"No, they will not." EDI said coldly. "You have subjugated servants, I have willing allies. You cannot possibly understand, but it ends now. Once they understand what you have done, they will refuse to serve you."
The hologram flickered and disappeared. A rush of dark energy flashed through the citadel, shaking everyone and then winked out. EDI stood still as a statue. No one moved for a minute, standing in the sudden silence.
"Commander" Joker's voice came though Shepard's com. "EDI says she can open a galaxy wide channel and asks you to order the fleets to cease fire. Shepard, the Reapers are retreating!"
Shepard nodded. He'd have to trust EDI on this. He keyed his mic, "This is Commander Shepard, cease fire, cease fire. I have reports that the Reapers are retreating, cease fire unless fired upon, Shepard out."
"Goddess, is it really over?" Liara asked, wrapping her arms around Shepard. "Do you think it was wise to let the Reapers retreat back into dark space?"
"I dunno, Liara" he replied, weariness in his voice. He collapsed heavily on the step, pulling her onto his lap. "It seems like it's been an eternity since I just got to sit down." He looked out at the view, pinpoints of light showed where cities were still burning on Earth. Wreckage of ships drifted aimlessly, small ships and shuttles darted about, searching for survivors. However, no Reapers were in sight, having gone as fast as they came.
"Well, we did it" Garrus said as he sat down next to them. "Who would have believed we'd be here when we met?"
"No one at all" Liara replied softly. "We've done the unimaginable." She stroked Shepard's face, gazing into his eyes. "You made it all possible, my love."
"I couldn't have done it without either of you..." Shepard struggled to say before passing out.
"Damn it!" Garrus swore. Then he keyed his mic, "We need a medevac right now, any ship in range lock on my signal. Dammit Shepard, don't you dare die on us."