1.
From Anderson's death and Hackett's call that nothing is happening with the Crucible:
Shepard collapses against the control panel - it whirs and lights up with activity. Shepard weakly pulls his head up then backs away - a display of immeasureable data fills the vantage point of Earth. Amidst the constantly flickering and cycling data, one constant: a blueprint-like image of Harbinger. Shephard, perhaps do to the cipher, seems to understand.
The player is able to investigate some of the data through Shepard and learns:
The Crucible isn't a weapon but a beacon attuned to recieve and transmit the collective history of every cycle that has been Reaped. (Beacon/cipher bookend with original Mass Effect) (transmission contained in dark energy?)
Every cycle completed their own Crucible which recorded their war against the Reapers and inevitable defeat / where they went wrong.
No previous cycle had ever been able to unify all of their diverse spacefaring races under one banner against the Reapers in time. (Reinforcement of Javik statement in regards to the Protheans and the theme of unification and cooperation against a universal enemy)
Passed down through every cycle and every completion of the Crucible is the information necessary for defeating the Reapers: "The Catalyst" is Harbinger, the original Reaper and de facto leader who resided over the creation of every Reaper and exerts it's will over all of them (indoctrination writ large?)
After finding this information, Harbinger enters. It attempts to finish off Shephard while mocking him. Still critically wounded, Shepard must avoid the laser and make his way to whatever may consititue an exit beam.
2.
Shephard's injured squadmates and the small remnants of Hammer have made their way down to the Citadel beam; Shepard is transported in front of them with the beam closing behind him. He radios Hackett and fills him in on the situation: Harbinger must be destroyed at all costs. Hackett informs Shephard that Harbinger is headed back down for another attack before giving the order for all allied forces to focus on Harbinger. (Bookend with Mass Effect and Sovereign)
3.
The fleets are hammered by Reapers as they break off their current attacks and bring all their guns to bear on Harbinger.
4.
Harbinger's shields withstand the impacts as it reenters the atmosphere and descends towards Shepard. The Normandy, Destiny Acension (If it survived Mass Effect), and a handful of other ships follow.
5.
From high above, Harbinger begins raining fire down on Shepard and Hammer. The player must survive as every shot bringers Harbinger closer. The better the player's EMS the shorter the battle, eventually Harbinger is overcome: if the Destiny Ascension is present, it sacrifices itself to deal the damaging blow, otherwise, the Normandy makes the final attack with an EMS check; failure results in the Normandy's destruction with Joker flying into Harbinger to bring it down, success sees the Normander crash land safely.
Harbinger is irreparably damaged and crashes into the city with a large explosion and shockwave, leaving it lying in a massive crater with a radius of barren land. (Harbinger's antagonistic vendetta against Shepard provided a unique opening that left it more vulnerable than in any previous cycle)
6.
After a moment of victory with Hammer and his squadmates, Shepard sees off in the distance that Harbinger is still functioning.
7.
Most of the allied fleets are in ruins, the Reapers' victory is at hand. Hackett's ship and what's left of his forces try to hold off the Reapers.
8.
Shepard is radioed by Hackett that Harbinger is still moving down there but the fleet is helpless to finish it. A desperate plan is hatched: a Thanix missile battery from Hammer has survived but Harbinger's weakpoint is protected from fire inside the crater; the battery is rigged to explode and someone must drive it into the crater while resisting the still active Reaper's indoctrination attempts.
It's a one-way trip and the player must choose either Shepard, Liara, Garrus, or VS for the sacrifice. (Each volunteer and Liara is always alive up to this point so the player always has at least one alternative). The chosen character recieves a send off from the others.
9.
The chosen character drives across the decimated plain as Harbinger tries to indoctrinate them. If Shepard, the player can choose dialogue responses to Harbinger, otherwise the chosen alternative responds uniquely to it's attempts. With sufficiently low EMS, an alternative to Shepard can fail, becoming indoctrinated and detonating the missiles prematurely - bad ending.
Success sees the payload delivered and the chosen character sacrificing his or her self. Harbinger is finished in a dramatic explosion.
10.
Above, in space, Harbinger's influence wanes: most Reapers, products and engines of genocide for untold cycles, begin to exhibit free will and, recognizing themselves as monstrosities, turn on each other to break the cycle once and for all (reinforcement of synthetics as living, free beings with a "soul", organic components reject Harbinger). Some of the oldest and largest Reapers stay true to Harbinger's motives and resist but are overcome by the others. The Reapers have destroyed themselves, with a scarce independent few peacefully departing for unknown destinations, they are free.
11.
Visual epilogue; character, race, and location fates determined by player choices throughout the series with EMS factored into survival.