Basic premise is this story follows the indoctrination theory. So after the beam knocks out shepard it all takes place in her (in my case) head, and picking the destroy option is the way to escape indoctrination. So this story picks up after the Shepard breathing scene.
Shepard woke with a gasp. Every nerve in a body felt like it was on fire as consciousness returned to her. Her green and white N7 armour was scorched and melted, her skin blistered and cut. Her breathing was painful indicating more than one broken rib. She was however still alive and relieve flooded her system, like a great weight had been lifted of her shoulders.
Was it over? She thought.
The sounds of battle still raged around her, as she looked up. The two kilometre form of Harbinger literally toward over her, its yellow 'eyes' seeming to glare at her.
"SHEPARD!" it bellowed, shaking the ground as it spoke, "YOUR EFFORTS OUR FUTILE AGAINST US. WE ARE ETERNAL!"
Shepard staggered to get to her feet as Harbingers main weapon began charging with its ominous red glow, gritting her teeth in agony she forced herself to stand.
Suddenly the familiar voice of Joker sounded over her com, "Hey! Asshole! Knock knock!"
The Normandy had been skimming over the rooftops of London since Harbinger had broken off from the battle. Its Silaris Armour scorched and dented from AA fire. As it cleared the last building a shining blue light collected at its nose as the Thanix cannons powered up.
Harbinger adjusted its position to get a clear shot at the Normandy but too late. A white-blue beam lanced from the nose of the Normandy striking exactly where Harbingers main weapon was located in between the gaps of its five legs. The Normandy which was travelling too fast to pull away instead hurtled straight towards Harbinger firing six Javelin missiles pointed blank before performing a barrel roll to avoid a collision by inches.
Harbinger screeched and wailed as its systems overloaded and red explosions dotted its hull before its back legs buckled and it tipped backwards making the ground shake and buildings collapse as it hit the ground.
"Oh yeah! WHO'DA MAN!" cheered Joker as the Normandy pitched upward, "Finish this Commander!"
Shepard grinned in spite of the pain, "Nice job Joker, wi-"
Before Shepard could finish her sentence, Harbingers corpse exploded in a crimson blast, the shockwave sending Shepard flying backwards.
Groaning in pain Shepard got to her feet again, looking around to see the damage. She spotted what she was looking for, Liara and Garrus.
30 feet away from her they lay unconscious in the dirt, she prayed they weren't dead. Running over to the them she check the pulse of the Asari first, steady and strong so just unconscious, then she check the Turian, how had a large rent in the torso section of his armour. His was fluctuating wildly, she quickly applied medi-gel to the wound to stabilize him.
"All hammer forces," called Hackett over the comm, "The conduit beam is unstable. You've got to get there now or this is all for nothing! Reaper forces are converging on your location, we've got Geth reinforcements for those who can't make the beam in time but someone get there now!"
Shepard whipped around to look at the beam, it was pulsing erratically get narrow then wide at random intervals as well as bolts of mass effect energy lancing into nearby objects.
Guiltily she turned to face her companions, "I'm sorry Liara." She said before kissing her lover on the forehead.
She looked at Garrus, "Meet me at the bar sometime."
Unholtersing her Paladin pistol and pushing through the pain Shepard took off for the conduit. The ear splitting shriek over hundreds of Banshees ran through her body as enemy troops converged on the conduit.
Within a minute Shepard crossed the wasteland to the beam and threw herself into it. The mass effect energy connected with her and in the blink of any eye accelerated her to the Citadel.
The area of the wards the conduit took prisoners to was dank and dark when Shepard was unceremoniously thrown into the room. The silence was only broken by the rapid intense beating of Shepards heart in her ears.
Lights of circuitry illuminated the walls around her; it pulsed rapidly with more and more of it turning red as opposed to blue. She guessed something was wrong with the system.
Unexpectedly all the lights suddenly flickered out before the room exploded in a shower of sparks. Shepard covered her face to protect it but then tore them away to look as a familiar screech met her ears in the midst of the overloads.
A Banshee had followed her through and from the looks over it the beam had failed on earth instantly afterwards.
"Oh fuck." Whispered Shepard as the Banshee glared at her.
In spite of the intense pain of her broken body Shepard dived away as the Banshee sent a biotic attack her way. Just missing her it buckled the wall behind.
"SHIT, SHIT, SHIT!" swore Shepard as she ran for the door.
It was to little use however as the Banshee performed its unique charge and she ran head long into it. It's skeletal left hand grabbed her around the throat and lifted her off her feet as the right hand drew back to perform its dreaded impale move on her.
Well what do you think as a start? Hope you don't mind long waits to find out what happens next as we're not coming back to Shepard for quite awhile. Most of the story will be the battle on Earth experiences by VIPs (mostly Shepards squad members both past and present). R and R. Enjoy.