Disclaimer: Mass Effect belongs to BioWare and EA. This is merely my take on the universe.
A/N: Quick background on Beinir Shepard (Default male appearance, except he's blonde):
Spacer.
Sole Survivor.
Soldier.
Mostly Paragon, but has gotten more cynical as time has marched on.
Recruited everyone to fight Saren.
Released Rachni Queen (Pragmatic - Saw her as an ally against the Reapers).
Killed the colonists and Shiala on Feros.
Ashley died on Virmire (Training kicked in – save the officer, not the enlisted soldier).
Completed Tali, Wrex and Garrus side missions.
Found Kahoku, eliminated all the Cerberus ops, Toombs killed the scientist and himself.
Saren suicided - Focused on Sovereign – Anderson on Council.
DIVERGENCES FROM ME1 PLOT/GAMEPLAY:
Brought entire squad with him on missions.
Had squad train each other to proficiency in assault rifles, decryption, electronics, and first aid.
Stole Saren's research data on Virmire to secure Wrex and the Krogan as allies for the Reaper War.
Took recordings of everything Prothean and Reaper related, especially on Virmire.
Murdered Udina in front of the Council after being informed of Normandy lockdown (They didn't like Udina, and the Turian Councilor finally saw that Shepard was worthy of being a Spectre. The lockdown lasted all of thirty seconds after the shotgun blast).
Set up care packages for himself and his ground team after Virmire, consisting of five million credits and Spectre X weapons for each person.
Tali came to see him before Ilos. No suit removal, but she comforted and inspired him.
PROLOGUE
Beinir Shepard was bored of hunting Geth. He never seemed to encounter any action needing himself or his ground team, so he was stuck doing busywork on SSV Normandy. He was glad that the mess was empty at that particular moment, because he needed his morning coffee before he slogged through the briefings on the latest incidents the Council had sent him to deal with.
He was looking over the reports of Geth sightings near someplace in the Terminus Systems, 'Illium, right?' The information was sparse, but apparently the synthetics had only been in-system long enough to change which direction they were taking the mass relay. The Council had sent him as a precaution, knowing that while the Normandy wasn't meant for stand-up fights, Shepard would call in the heavy hitters.
Beinir had just set his mug down when Joker shouted over the intercom, "Brace for evasive maneuvers!" Seconds later the ship rocked, spilling his coffee onto the datapad and shorting out the poor device. He managed to stay in his seat, then ran over to his locker to get his Colossus X armor.
Tali'Zorah nar Rayya was in the elevator, which she had modified to go faster just after she came on board the Normandy, on her way to the mess when she heard Joker on the intercom. She was sent sprawling when the ship took the first hit, but she got out of the lift and ran for Shepard's quarters. Before she got there, she noticed the man sprinting over to the control panel near the sleeper pods. She took off in his direction and shouted through the fire and flames, "Beinir!"
Beinir secured his helmet and told Tali, "Distress beacon is ready for launch."
She frantically asked him, "Will the Alliance or Council get here in time?!"
Another explosion, then he tossed her a fire extinguisher and they both started trying to put out the fires. Shepard replied, "Not bloody likely, knowing their slowness. Tali, I need you to get everyone to the escape pods."
She reported to him, "Joker's still flying, he won't abandon ship." A moment later she added, "I don't want to leave you, Beinir."
Shepard, ever the one to look after his crew, told her, "I'll take care of Joker, you get everyone out of here, yourself included."
"I-"
He turned to look her in the eye and gently but firmly ordered, "Tali, go. Now."
Dismayed, she answered, "You got it, Beinir."
Tali ran to the nearest pod along with several other crew members and ushered them in, yelling, "Everyone in! There's not much time!" One servicewoman was caught in an explosion and died before she hit the floor. Tali climbed in the pod and hit the button to eject. As the panel covering the pods swung out she wondered, 'Why didn't the Alliance use exploding bolts instead? It would be much faster.'
Shepard ran through the smoke while Joker sent a distress signal of his own. "Mayday, mayday, mayday, this is SSV Normandy! We've suffered heavy damage from an unknown enemy!" The door opened, and the remaining atmosphere was sucked out into space. Shepard silently thanked Kassa Fabrications for putting electromagnets in the boots of his armor as that was the only thing preventing him from being sucked out as well.
When Beinir reached the cockpit, he wasted no time, hefting Joker over his shoulder in a fireman's carry while telling him, "Sorry about the rough ride, but we gotta go!" He threw the pilot into the remaining escape pod and was almost in the pod himself when he felt an insane amount of heat in his legs. An explosion knocked him into the pod, and Joker hit the eject button.
The pod launched, and both men saw the attacking ship carve up the Normandy like a tender roast and leave. The last thing Joker expected was his commander's blood-curdling cry of pain as he looked and saw that Shepard's legs had been severed at the halfway point between his groin and his knees.
The hour it took for the Alliance cruiser SSV Manila to rescue the surviving crew from the Normandy was the most excruciatingly painful hour of Beinir Shepard's life. When Doctor Chakwas and the Manila's medical crew made it to his pod, he was on the brink of passing out from the pain. The voices around him were fuzzy and far away, but one was clear.
Tali saw Shepard being pulled from the pod... or rather, most of him. 'Keelah, his legs are gone!' She immediately ran over to him and promised him, "You stay with us, Beinir, I'll help fix you up!"
He took off his helmet, weakly told her, "You're a sweetheart, Tali, but you have a Pilgrimage..." before he finally passed out on the hovering gurney on his way to the Manila's medical bay.
Chakwas raised an eyebrow and Tali responded, "The Migrant Fleet can wait. Shepard needs my help." She lowered her voice so that only the two of them could hear, "I care about him too much to just leave."