I decided to try to write a MShep/Kaidan alternate ending. Plus what happens after the Reaper War in ME3. Rated T for occasional language and probably future content. Rating may change later on. Anyway here it is.

No Matter What

"The Crucible isn't firing, Commander," Admiral Hackett's said over the communicator. "It must be something on your end."

Every muscle in John's body screamed in pain, but he knew he had to do something. "I-I don't… I can't…" He struggled and crawled toward the consol.

"Commander?" Hackett called out to him.

He forced himself up. He could feel the darkness creeping up on him beginning at the back of his head. He was going to pass out, very soon. Spots started appearing in his vision as he haphazardly worked on the consol. He could feel himself collapsing, not knowing whether or not his meager effort had made a difference.

"I-I'm sorry," was all the commander was able to choke out before he finally passed out from the exhaustion and pain.

But the Commander was successful. Somehow he had managed to engage the Crucible's firing mechanism.

"The Crucible is firing! All forces disengage and fall back to the rendezvous point." Hackett ordered over the com.

The Normandy was still actively assisting in any form it could.

"We have to go Joker," Garrus put his hand the pilot's shoulder.

"Yeah." He replied regretfully. "I know."

"What about Shepard?" Liara burst into to cockpit.

"We have our orders Liara," Joker said.

"Since when have you been one to follow orders?" Liara replied smartly. "We can't leave the Commander behind again."

"Dammit Liara," Garrus said, "We have to go!"

"No," Joker interrupted, "She's right. We have to stay. He's OUR commander."

"Well it's too late now," Garrus looked out the window. In the distance a white light was expanding rapidly from the Citadel.

"Everyone hold on tight!" Joker hollered.

Within seconds the Normandy was enveloped, and the ship immediately went haywire. Sensors and systems where powering up and down, alarms were sounding. Fortunately EDI was able to keep the essential systems stable.

"Multiple system failures," EDI scrambled to retake full control. "Rerouting power to essential life support systems."

"Come on EDI," Jeff encouraged her, "We can do this."

"I have to reboot many of the systems." For a moment the entire ship went dark. The entire crew held their breath as EDI restarted the ship. The seconds slipped by, each seeming to last an eternity.

"All systems back online," EDI announced as the ship regained power.

Joker took over, "let's go get Shepard," and he directed the ship towards the Citadel.

Reapers were everywhere, still and silent, their empty shells drifting in the vacuum of space. It was eerie to see them like that. The unstoppable force that was bent on the destruction of all advanced life just a few moments ago, was now gone. They almost looked peaceful. The civilizations that came before were now allowed to rest.

As Joker navigated through the disabled Reapers, Dr. Chawkwas had her hands full down the med bay.

"Kaidan, you need to calm down," she ordered the Major, "I need to see if there was any damage to your implant. You've already had one close call."

"I'm fine, I just need you to get me on my feet again." He was frustrated. He wasn't going to be stuck in a bed again when he could be doing something to help. "I-I can't just sit back and watch this time." His eyes were full of emotion.

"No matter what happens, I love you Kaidan." It was everything he could do not to fall apart when thinking of that moment. John was out there, and he needed to get to him.

The doctor sighed and nodded, understanding what he meant. "You still have to sit still while I look at your leg." She got to work helping him take off his armor, so she could fully examine his injuries.

After a few moments she gave him the news. "Well Major, I can patch you up and get you on your feet, but you have to promise me you won't push yourself. Otherwise, you'll just wind up here again."

Chakwas got to work, while the Normandy approached the Citadel. A few minutes later James entered the med bay.

"How you holding up, Boy Scout?" he asked Kaidan.

"A little worse for wear, but Dr. Chakwas says I'll be up pretty quick." Kaidan replied.

"It's a good thing the Commander was able to negotiate a trade with the turians. You may have been out of luck if he hadn't," Chakwas commented.

"I just came to tell you, that we'll be arriving at the Citadel in five minutes," James said. "We're organizing a group to look for the Commander and other survivors."

"Just give me a few more minutes." Dr. Chakwas finished her work as quickly as she could, sensing that Kaidan was eager to leave the med bay as soon as possible.

He winced as he put pressure on it for the first time.

"You all right, Boy Scout?" James inquired.

"Yeah, Yeah. Let's just go." Kaidan put on his alliance uniform and limped out of the med bay with the lieutenant. His leg was stiff and sore from the medigel treatment, and his side ached. There was a giant bruise on the left portion of his ribcage, but no other serious damage. He was moving slower than usual, but nothing would stop him from reaching from the Commander.

The entire squad was gathered in war room, looking at schematics of the Citadel. Liara was explaining the plan to everyone.

"Our best estimate is that the Commander and Admiral Anderson are located here," she pointed at a highlight section of Citadel, near the docking point of the Crucible. "No one has been able to successfully communicate with them for some time. The Normandy will dock at this location," she pointed to another location small distance away from Shepard's location. "A small team will take the shuttle closer to our target area."

Garrus, Liara, James and Kaidan chose to take the shuttle while everyone else stayed on the Normandy. Liara pulled Kaidan aside before they boarded.

"Are you sure you want to go Kaidan?" she looked him straight in the eye. "We don't know what we'll find down there."

"I have to Liara, I have to know. I have to know what happened to him. If he's alive or…" Kaidan couldn't finish and lowered his gaze, no longer able to look into Liara's piercing blue eyes.

"Okay," was all she said. She gave him sympathetic look, and placed her hand on his shoulder before she got on the shuttle. Kaidan took a deep breath and followed her.

Everyone was silent on the short trip down, trying to prepare themselves for whatever they would find. Kaidan was hunched over in his seat eyes closed, focusing on the task ahead. He was trying to prepare himself for the worst, but he knew there was no way he'd be fully ready, should his worst fear become real.

The thought of finding John's lifeless body was almost more than he could take, but he knew he had to go through with it. He had to know. He had to. He didn't want to hear about it second hand like he had the last time. Then only come to discover that the Commander had been brought back. He wouldn't be able to handle another mind fuck like that. He had to see for him self. He had to know.

The shuttle landed just outside the room they were headed for. A giant chasm and a bridge was all that separated the team from their Commander and the Admiral. As soon as the doors opened, Kaidan moved a quickly as he could towards the center room. A moderate jog was all he could manage, and the rest of the team followed suit.

Kaidan felt his stomach drop the moment the room came into view. The room was very large and the viewing windows showed an impressive view of Earth. But Kaidan wasn't there to admire the view. Three motionless bodies lay at various places on the floor. He immediately recognized the charred armor of the body closest to the windows. Shepard.

He raced over to him. Carefully he rolled him onto his back and to his great relief saw that he was breathing. It was ragged, but he as breathing nonetheless. Desperately trying to hold back tears of relief, Kaidan knelt beside him, and against his better judgment, cradled the Commander's head in his lap. To Kaidan's surprise, Shepard opened his eyes.

"K-Kaidan?" the Commander choked out, struggling harder for air. His armor was in shambles, one of his arms was badly broken, not the mention the countless bruises and cuts. Kaidan could even see some evidence of his cybernetics that he couldn't before. His eyes now had an eerie yellow glow behind the normal green Kaidan had come to love.

"Shhh," Kaidan was trying even harder now to keep the tears back, "Don't talk, you're okay. You're going to be alright."

"No… I-I'm not," Shepard choked and coughed. A dribble of blood escaped the corner of his mouth. The rest of the team looked on helplessly.

Kaidan couldn't hold the tears back anymore, this was worse than finding him dead. "Don't say that. I'm here. Don't give up on me now."

"I'm so… Tired Kaidan. I can't…"

"You have to! You can't leave me like this! You didn't give up on me, I'm sure as hell not going to let you die. Stay with me…" Kaidan was sobbing now.

"Kaidan," Shepard caressed Kaidan's face with a bloodstained hand, "I-I love…" Kaidan took his hand, and Shepard's eyes began to close again.

"No, John. Stay with me! John!"

The rest of the Normandy team arrived. Kaidan was pulled away, and the Commander was taken away on a stretcher. The crew turned their attention to Admiral Anderson, who was confirmed dead. As was the Illusive Man. Their bodies were also taken back to the Normandy.

Kaidan and the rest of the squad waited in the mess hall while Dr. Chakwas worked to stabilize the Commander. The med bay window's shutters were closed, as to not alarm the crew to what went on inside.

They waited in silence. Tali leaned into Garrus for support, who in turn put his arm around her. Everyone was there, even Javik still in the far corner waiting for news. All were on edge. The war was won, but the struggle was far from over.