A week after taking Chronos station, Hackett tells Shepard they've got it, they know what the catalyst is. The Citadel itself is the catalyst. He tells Shepard they're massing all the allied fleets to secure the station so the crucible can be brought in.
It only takes one indoctrinated traitor among the fleet to tip off the Reapers to the plan and suddenly it's a race to the Citadel. The massive allied fleet has the mass relay tied up so the Reapers use their superior FTL drives to come in from an adjacent system. The two massive fleets reach the station at the same time.
While the largest scale space battle in history rages, tens of thousands of shuttles and drop ships from both sides rain down all across the station. Hundreds of thousands of troops begin a desperate fight to secure the station. It quickly devolves into absolute chaos.
Shepard leads the squad up the presidium tower once again. They need to reach the main control terminal in the council chambers to fire the crucible.
The fighting is brutal, the Reapers are pouring as many ground troops as possible in to stop them, using the keeper tunnels to stay ahead of him every step of the way. While fighting their way up, Shepard has taken a horrendous amount of damage. He has over a dozen wounds from gunshots, shrapnel, burns and claws but he pays them no mind. His pain is irrelevant.
As they're fighting their way up the council chamber towards the terminal, Shepard sees a Ravager on one of the balconies above them taking aim at Jack, who doesn't see it. He tackles her to the side, taking the shot for her. His shields take most of the blast but the round still blows a massive hole in his side. They roll to a stop in cover off to the side of the room. He nearly panics when she doesn't move. He runs a scan with his omni-tool and is relieved to find she should be okay, she's just out cold.
The rest of the squad is pinned down across the room but Garrus manages to get over to them. Shepard struggles but manages to tear his eyes off of Jack and looks to Garrus.
"Get ready to cover me to that panel."
"You'll never make that run alone, I'm going with you."
"No, you're not."
"Garrus, I need you here, with her. I need to know she'll be okay."
Garrus doesn't want to let Shepard run the gauntlet alone but knowing how important Jack is to him, he nods in agreement.
Shepard breaks cover and runs for the panel. The squad covers him and he makes it, but not without taking a round in the shoulder. If he feels it at all, he doesn't show it. He activates the panel and follows the instructions recovered from the beacon. Rather than fire the crucible, the platform he's on begins to lift into the ceiling.
He ends up in a part of the Citadel no one even knows exists. In front of him, down a long sterile hallway, is a ramp that leads up into a large round room with an unobstructed view of the unparalleled destruction going on in space. As he's walking up the ramp, he stumbles. He collapses at the top, his wounds catching up to him. He forces himself to his feet and limps to the control panel at the other end of the room.
He reaches it and a holographic display pops up. It's in Prothean but thanks to Javik he can read it. After a moment he has his hand over the button that will end the war.
With Shepard so close, the Reapers get desperate. They throw all of their might into one final attempt to seize control of his mind to stop him.
Rather than punch that button, Shepard hesitates.
All that death and destruction, just for it to end with one button.
That's all it will take.
Should I though?
What if they're telling the truth?
What if they really are trying to make us something more?
Who am I to take an opportunity like that and throw it away for everyone?
Back down in the council chambers, the squad is fighting desperately to hold the room but with Shepard gone they can't keep it up for long.
Jack finally stirs and wakes up. She looks around desperately but can't see Shepard anywhere. She grabs Garrus and demands "Where the fuck did he go?!"
"He hit that panel and it took him up into the ceiling."
They're pulled back into the fight when a fresh onslaught of gunfire hits their cover. Garrus speaks to the whole squad.
"We can't keep this up, we need to fall back!"
Jack is outraged.
"What?! We're not fucking leaving him!"
"We don't have a choice, we can't hold this position."
"If you don't have the balls, then fine, fuck off! But I'm not leaving him on his own!"
She breaks cover and charges for the panel, ignoring the surprised shouts from the squad. They redouble their fire to cover her. She makes it, barely, and follows Shepard up.
With Shepard and now Jack gone, the squad can't hold their position. They hate to do it, but they have to fall back, hoping Shepard and Jack can handle themselves.
Jack walks down the hallway warily. She climbs the ramp and sees him standing there, paralyzed. She calls his name but he doesn't react. She steps up next to him and sees he has his hand over the control panel, she can't read it but she gets the idea.
When he hears her voice, it all comes flooding back to him. The Reapers are still trying their hardest to stop him but as he looks into Jacks eyes, his resolve becomes incorruptible. She takes his outstretched hand and gives him a nod. Together they firmly press the button.
When they press the button, the Citadels arms open wide, extending to their full length. Seeing this, Hackett brings in the crucible, knowing they won't have long. Hundreds of ships sacrifice themselves escorting it to the station but somehow, the crucible reaches the Citadel unharmed. When it docks, it sends a signal out across the relay network.
The spinning cores of the relays farthest from the Citadel begin spinning faster and faster, the light coming from them growing in intensity. Once they're charged enough, the cores abruptly stop spinning and all the energy stored within, a truly astronomical amount of power, is fired off to the next relay. This continues, the power levels snowballing until every relay in the network has pooled their power sources into one.
The Citadel rotates, facing directly at its relay. A blinding beam of light blasts forth from the relay to the station, utterly vaporizing any allied or Reaper ships in its path.
The station rumbles as it channels an unknowable amount of energy into the crucible. Once it's fully charged, the crucible releases the energy in one massive red blast. The wave moves at such a ridiculous speed that it only takes a day and a half for it to cover the entire galaxy.
When the wave passes over Reaper ground forces, they drop dead on the spot. When it passes over Reaper ships, their circuitry is completely burned out, leaving only an inert hulk. As it passes over allied ships and people, nothing happens. Any indoctrinated people die instantly of severe brain hemorrhaging and any computers holding Reaper code are burned out.
Back in the control room, Shepard and Jack look down at the panel in front of them, not sure if hitting that button had done anything. Jack is let down.
"The fuck, it didn't work."
"No, look at the screen, something's going on with the relays."
"That shit's in Prothean so I'll take your word for it."
They look out at the carnage surrounding the station for a moment while the crucible does its thing. Jack looks over at him when she hears him grunt. He's pressing his hand to the gaping wound in his side but there's still a river of blood pouring out. She rushes over just in time to catch him as he falls. She lowers him to the ground, cradling him in her arms and trying to help stop the bleeding. Tears form in her eyes when she realizes they're both out of medi-gel.
"No, no, John, hold on!"
"Jack, I, I-"
He coughs hard, hacking up blood.
"John, no, please…"
When he stops coughing he reaches up and cups her cheek. He tries to brush away her tears but they're coming too fast.
"Jack, I love you."
"I love you too you asshole! So don't you dare, hey, no, wake up! Wake up! No!"
She shakes his shoulders desperately but his eyes don't open. She wraps her arms around his head and holds him tight, sobbing uncontrollably.
It takes two hours before the squad finds them. They break into a sprint when they hear Jack wailing in the distance. When Jack hears them approaching, her biotics burst to life, a corona of blue energy rolling off of her.
Waves of biotic power begin to buffet the squad from as far as a hundred yards out. They struggle to press forward but the constant barrage makes staying on their feet all but impossible.
As Miranda is his best chance at surviving, Samara adds her own biotics to Mirandas barrier. Liara and Javik catch on and add their own. With their help, Miranda is able to force her way forward. Twenty feet away, she yells at Jack.
"Jack! Stop, he's alive!"
Jack is too absorbed by her grief to listen. Instead, the sound of someone getting close causes her to release an even more powerful wave. Miranda skids back several feet but manages to keep her footing.
She trudges forward and reaches them. As Miranda kneels next to Shepard, Jack squeezes him tighter and yells without looking up.
"Fuck off, you're not taking him!"
Miranda reaches out and cups Jacks face, forcing her to look up.
"JACK, HE'S ALIVE!"
Her eyes go wide with disbelief. The biotic hurricane stops abruptly, allowing the rest of the squad to come forward. She lays him down on the ground, cradling his head in her lap. Miranda immediately gets to work stabilizing him. Rather than try to deal with his numerous wounds, she liberally fills the holes in his armor with medi-gel. Garrus and Liara help, the others set up a perimeter.
When Miranda decides it's safe enough to move him, Samara lifts him off the ground, focusing all of her considerable skill on keeping him perfectly still. They make their way back to the lift as quickly as they can. There isn't much room on the lift, only Miranda, Samara and Jack are able to go down with him. There are several medics waiting to receive him. As they whisk him away, Jack moves to follow him. Miranda puts her hand on Jacks shoulder to hold her back, the single most dangerous thing she's ever done in her life.
"Jack, the best thing you can do for him now is to let the doctors do their job."
"Let go, I need to be with him!"
"You already did all you could, you kept him alive. Now it's up to them to fix him."
Jack stands stock still for a moment before storming off without a word.
The battle lasted a little longer than six hours. Almost two million ground troops landed in that time. Estimated casualties on the station were one million soldiers and two to three million civilians. The fleet suffered over seven million. They had thrown themselves straight into the enemies jaws, trying merely to be in the way long enough for the crucible to be deployed.