Finally I've decided to start to write my own headcanon ending for Mass Effect 3. This was my idea since the first time I've finished the game. After the EC DLC and Leviathan DLC, I've just added some new parts.
I've changed many things because I didn't like at all any of the original endings. Though, I didn't mean to offend anyone who likes them, everything I wrote here is only my opinion, but I totally respect other people's preferences!
I've been inspired by the 'indoctrination theory', but I've developed it in a personal way.
I have to thank my lovely amazing super friend Mandy, who's helping me so much with my fics, checking my English and giving me great suggestions.§
I hope you're going to enjoy it! ^_^

Chapter 1

12/20/2186 – Normandy SR-2

No… Not again… Not… again…

"… enko?"

Not again… please…

"… jor Alenko?"

Please… I can't… Not… again…

"Major Alenko! Do you hear me?"

Not again…

"KAIDAN!"

He opens his eyes and he's in the medbay, aboard the Normandy.

"Doctor Chakwas?" He stares at her confused, his sight blurry.

"Oh, finally. You were unconscious for about… 15 minutes."

"Wh-what… what happened?" He tries to sit but his head is spinning. "Why am I here?"

"Don't move Kaidan. You're badly injured." Another voice floods the room.

"Garrus…? What…?"

"You were knocked down by a Mako thrown by Harbinger's beam. It almost hit your head, it's a miracle that you're alive…"

All at once his memories of the last hours came back to him – the fight in London against all those husks and then the rush towards the beam that would lead to the Citadel. They were almost there when the incident had happened. And now he's here while his soul mate is somewhere else alone, trying to make the Crucible work.

"Normandy! Do you copy?" Shepard is shouting at her comm-link. "I need an evac. Right now!"

She turns her attention to him. "Kaidan, they'll be here any second. Come on!" With Garrus' help, she hoists him on her shoulder.

Soon the Normandy arrives on the battlefield, evading Harbinger's beams. They run towards the hatch of the Shuttle bay, but when they get there, she lets her grip on Kaidan loose.

"Garrus, take him." She starts to back off.

Alenko is immediately caught by a terrible fear. "Shepard! Where are you going?"

"You have to get out of here," she answers him, gesticulating to make her point clear over all the loud noises of the battlefield.

"Yeah, that's not gonna happen!" He can barely breathe from all the pain and the blood loss, but he can't even consider not being at her side now.

"Don't argue with me Kaidan." Her sky-blue eyes give him a serious look through her visor and her tone is so imperious that it makes him gulp.

"But, Shepard…"

She sighs as her gaze turns gloomy. "I am sorry, but I have to be rude… Kaidan, you're wounded and I can't take you with me. You wouldn't be of any help at the moment, and you know I'm right."

He feels his eyes filling with tears. "Sharilin, please… Don't leave me behind again…"

At his last words, her face twists in pain. She knows he's thinking about that damned day when the Normandy SR-1 crashed. She had forced him to leave with the crew while she had gone looking for Joker. And then she had died…

She approaches him again. "Kaidan, do you remember what I've said to you before?" She gives him her sweetest smile. "I need you to take care of your injuries now, because when this is over, I'll be waiting for you, you have to come and find me."

A single tear spills from his eyes. "I will, Sharilin…"

She raises her left hand and caresses his bloodstained cheek. "No matter what happens… know that I love you, Kaidan. Always…"

"I love you, too…" He smirks shyly back to her. "Be careful…" He tries to grab her hand but she's already moving away from the ship, yelling at them to go.

Not again, my love… Please… Not again… Alenko bends down on his knees, his hands gripping his head. He's terrified by the idea of her dying a second time. He can't live without her anymore. The first time part of him died with her and he started to breathe again only when they got back together.

Suddenly his train of thought is interrupted by another reminiscence: Shepard's expression before the Normandy blew off. She was grinning and the look on her face was sure and firm. She seemed convinced she would be able to end this war and she promised him she would be waiting for him.

Then he remembers the words she had said to him that night, after they had found Leviathan.

"My love… We're going to face the most dangerous enemies the galaxy has ever seen… But I strongly intend to win this war, and to survive at any cost."

"I've already lost my life, and also you, once… Then somehow I've obtained a second chance, and there's no way I'm going to waste it. So we'll defeat the Reapers and then we'll finally be able to start our life together."

The man inhales deeply. You're right, my love. We can do it. I believe in you, I know you're going to save us all again and then you'll come back to me. So I have to do my best, too.

"Doctor Chakwas, please patch up all my wounds as soon as possible. I have a ship to lead," he asks, returning to sit normally.

"I've already administered all the medication needed, but for now you have to r–"

"No way. I will rest when the war is over and when the Normandy has its CO back. Please, give me all the medigel you can, I have to get up right now."

A terrible migraine is beginning to torment him, though he doesn't care, he just needs to be active again.

"Ok Major, I'll do my best." Chakwas knows how stubborn he is, so she gives up immediately and starts doing her job.

"Garrus, how's the situation at this moment?"

"Pretty rough, Kaidan. All the ground squad around the beam is being evacuated, because the Harbinger is shooting everywhere. I don't even know how Joker was able to fly away with this ship without being hit…"

"And… Shepard?" He can barely pronounce her name.

The turian sighs. "We… We haven't had any communication from her since we left her down there…"

The Major's heart almost stops for a moment. "No-nothing?" he stutters.

"No… But this should be a good sign. You know what they say 'Bad news travels fast'… Besides it means that she reached the Citadel. She can do it, Kaidan."

He tries to force back his tears. "Yes, she can…"

"Ok, Major. I've done everything I could to medicate you. I will not tell you anymore that you need rest, but please, take care of yourself." Chakwas gently pats his arm.

"I will, I promise Doctor. I have to be at top shape because I have to rescue Shepard," he reassures her. "Come on Garrus, we have a war to win."

"Joker, how's it going here?" Alenko asks as he enters the cockpit.

"Kaidan! We're done with the evacuations and we're waiting for orders now."

"What do you want us to do, Major?" EDI questions him.

He brushes the nape of his neck, where his amp port is. His migraine is getting worse, but there's something he needs to do first. "Joker, patch me through the whole ship. I want to speak to everyone."

The pilot fulfills his request. "There you go."

Kaidan takes a deep breath. "To the whole crew, this is Major Alenko's speaking. I'm taking command of the Normandy for now, but this is Commander Shepard's ship and it always will be."

At his own words his stomach stings. "Some of you have been with her since the beginning, others are quite new to her team… But every single one of you knows Shepard well and you all saw she always fought for our safety – against Saren, against Sovereign, against the geth, against the Collectors… and she never stopped. No matter what kind of problems she stumbled upon, she kept carrying out her duties with all her bravery and courage."

He turns to look at Joker who's nodding silently. "Now she is out there, somewhere in the Citadel, trying to find a way to finish this terrible war once and for all thanks to the Crucible… So, w–"

A terrible rumble abruptly interrupts him and the ship begins to jolt, making the Major fall on the floor.

"Joker, what's happening?" he asks, trying to get up.

"Harbinger! It's shooting near the beam again!" Moreau yells.

The beam? Goddamn no! Shepard!

"Nor… ptzzzz… do y… opy?" A voice comes from the comm-link.

"This is Normandy," Joker answers.

"…ndy this is Alli… peaking… you hav… ack off."

"What? Back off? Are they kidding?" Alenko shouts astonished, "No! Never!"

The pilot doesn't look at him but shuts down the communications. "Awww… I'm afraid Harbinger has compromised our comm-link!"

EDI, who is seated near him, intervenes, "No Jeff, it's still w–"

"Shhhhhhh EDI."

"Oh… I see…"

The biotic approaches his friend again, leaning a hand on his shoulder. "Joker…"

"Kaidan, there's no way we're leaving Shepard alone… Not after all we've been through together… Never. You know, we're not famous for following orders." He winks. "But now I think you need to finish your 'inspirational speech', Major."

"Yeah, you're right…" He clears his voice. "People of the Normandy! The Alliance wants us to back off from the battlefield. But this isn't going to happen." His commanding tone is firm and persuasive.

"Shepard is out there alone, fighting for us and they want us to abandon her. There's no way. She would never abandon anyone of us. We need to find a way to support her, until we're able to rescue her. I need to know now if you're all with me in this."

A faint beep warns him that the door for the CIC is opening. James Vega enters the cockpit and stops in front of him, making the salute gesture. "Sir, all the crew will follow you till the end. This war ends today and we're bringing our Commander back."

Kaidan smiles, relieved, to the muscular soldier. "Thank you, Lieutenant…"

"So, what we're going to do now?"

"Unfortunately we can't reach Shepard at the Citadel, but there's something we can do to help her from here…" Alenko turns his attention again to Joker. "Come on, your moment has finally arrived. Show us your amazing piloting abilities. We're going to chase the Harbinger."

"Oooooooooh yes! Great! It's time to dance, baby!" He exclaims excitedly.

"James, come with me," the Major says, leaving the cockpit. "We're going to the Main battery to see if Garrus needs help with his Thanix cannon."

They pass near a group of soldiers in the CIC and one of them yells, "For Shepard!"

Soon the rest of the crew follows him, "FOR SHEPARD! FOR SHEPARD!" and making Kaidan stand still, amazed and moved.

Can you hear them, Sharilin? All your crew is here for you. Do what you have to do, and then hang on, we'll bring you back home, my love.