This is how I feel the game should have ended. I apologize if it is hard to follow, I typed it up in an outline format and it did not transfer over as intended.
1) (if <60% of total ground forces war assets were acquired and Shepard researched 9/9 cybernetic, medical & shield upgrades in ME2)Story as written at release with the exception that if the control/synthesis options were selected the mass relays were not destroyed. 1.A) Shepard, if he chose to destroy the Reapers, will wake up after the scene where the Normandy crashes. Shepard wakes up to see his current squadmates firing at the reaper forces above him before another blast from Harbinger envelops the screen and they all die. (If there were insufficient war assets for Shepard’s squad to survive to this point, two alliance marines would be in their place.) 1.B) Shepard, if he chose to control the Reapers, will wake up after the scene where the Normandy crashes. Shepard wakes up in a transparent pod to a similar sensation as when within the Geth collective but everything is tinted blue. Shepard hears many voices screaming simultaneously, not in his ears, but in his mind. As the realization that he is now a part of a new reaper comes to him, a look of horror appears on his face. The camera zooms out quickly, showing countless other humans in pods screaming, continuing with the camera traveling outside through two blue lights(reaper eyes?) on the form of a new reaper “gestating” from within the Citadel and moving further out through the citadel and onto the “Sword” fleet battling the Reaper armada. 1.C) Shepard, if he chose synthesis with the Reapers, will wake up after the scene where the Normandy crashes. Shepard wakes up being resting atop a “Dragon’s Tooth” being held in place by two husks. As the husks release him, Shepard is impaled by the devise. 1.D) (if Shepard had <95% of total fleet based assets were acquired and <95% readiness rating was achieved) 1.D.i) Hackett listens to the radio transmission that would have been heard during Shepard’s slow motion walk into the transport beam. The “Sword” armada continues its battle as Hackett comes over the radio and announces that the “Hammer” has failed but comments on this being the best shot they will ever have and orders the fleet to continue firing. Some of the fleet will continue fighting and some will flee from the battle(based on the percentage of total fleet war assets acquired). 1.D.ii) Joker, if the Thanix cannon and Silaris Armor and Cyclonic Barriers upgrades were not ALL taken in ME2, the Normandy is engaging a reaper dreadnought and is hit by the reaper’s main weapon. The hit does massive damage, the Normandy catches fire and Joker yells as he accelerates and tries to Kamikaze the Reaper but is hit again by the Reaper and the Normandy is destroyed before impact. Fade to black. 1.D.iii) Joker, if the Thanix cannon and Silaris Armor and Cyclonic Barriers upgrades were ALL taken in ME2, the Normandy is engaging a reaper dreadnought and is hit by the reaper’s main weapon. The hit does minor damage, the Normandy continues its strafing run before disengaging. Fade to black. 1.D.iv) More destroyers land near the transport beam and fire upon the remaining “Hammer” forces. 1.D.v) Kaidan, if he survived ME1 and survived Priority: The Citadel II and did not rejoin Shepard’s crew, will be seen leading a squad of N7 biotics falling back from the transport beam. The squad is wiped out by a blast from a destroyer. 1.D.vi) Ashley, if she survived ME1 and survived Priority: The Citadel II and did not rejoin Shepard’s crew, will be seen leading a squad of N7 marines falling back from the transport beam. The squad is wiped out by a blast from a destroyer. 1.D.vii) Miranda, if she survived ME2 and Priority: Horizon, will be seen stopping mid-charge. A destroyer’s energy blast blows up a mako in front of her, flipping it over and crushing her. 1.D.viii) Zaeed, if he survived ME2 and was loyal and Citadel: Volus Ambassador was completed, is seen coordinating sniper fire from atop a building. He turns to see a destroyer charge and fire its main weapon at them. 1.D.ix) Grunt(and Wrex if he survived ME1), if he survived ME2 and Attican Traverse: Krogan Team, is seen advancing through Reaper troops with a Krogan squad. The team is overwhelmed by the reaper troops. 1.D.x) Samara, if she survived ME2 and Kallini: Ardat-Yakshi Monastery, is seen with a squad of Asari Commandos fighting a group of Banshees. The Banshees charge in close and impale Samara through the chest. 1.D.xi) Shepard’s crew, if they were not taken on the final mission, will be seen behind cover firing on the advancing Reaper troops. The endless wave of reaper troops gradually closes in despite how many are killed. Fade to black as one reaches the squad’s cover. 1.D.xii) Fade from black. A mostly static radio transmission from Hackett is heard stating that “Hammer” has failed, the citadel armada has been crushed, and that their last hope to defeat the Reapers has been lost before continued static; the camera fades in to stars and pans over to see the wreckage of the fleet and a comm. buoy before the Reaper surrounded citadel opens up to “birth” a new Reaper Dreadnought from the collected Human population. The message begins to repeat but the screen cuts to black. 1.E) (if Shepard had ≥95% of total fleet based assets were acquired and ≥95% readiness rating was achieved) Hackett listens to the radio transmission that would have been heard during Shepard’s slow motion walk into the transport beam. The “Sword” armada continues its battle as Hackett comes over the radio and announces that the “Hammer” has failed but comments on this being the best shot they will ever have and orders the fleet to continue firing. Some of the fleet will continue fighting and some will flee from the battle(based on the percentage of total fleet war assets acquired).Hackett coordinates fire between the whole “Sword” fleet, focusing the firepower of 1/2 or 1/3 of the fleet on a single reaper at a time. Despite taking their own heavy losses, one by one the Reapers in orbit are destroyed. Some of the “Sword” fleet descends into the atmosphere and assists “Hammer” forces by destroying any remaining destroyers. Fading from black, Hackett is seen standing in front of the Normandy’s memorial wall(Shepard’s name, as well as the names of all of his crew from ME2 and ME3 can be seen on name plaques). After a few moments, Hackett turns and walks into the elevator on deck 3, then immediately out of the elevator on deck 2 before walking up to the CO’s platform, and(camera looking up at him from below the galaxy map) requesting status reports from Joker, Traynor, and the other Admirals before stating “There is a lot of work to do, so let’s get to it.” Cut to image of the Normandy and zoom out to reveal what was left of the fleet, the wreckage of the battle, and the Earth.
2) (if <60% of total ground forces war assets were acquired and Shepard did not research 9/9 cybernetic, medical & shield upgrades in ME2)Story as written up through Harbinger’s energy beam disabling Shepard on his way to the transport beam. 2.A) (if Shepard completed all character development/loyalty missions in ME1 and ME2 and the current squad is still alive) A current member of the squad(Love interest>Garrus>Tali>Liara>Virmire Survivor>EDI>Vega) calls out Shepard’s name and runs over to his downed body before hearing a reaper klaxon, and looking up to see Harbinger charge and fire its main cannon. 2.B) (if Shepard had <95% of total fleet based assets were acquired and <95% readiness rating was achieved) 2.B.i) Kaidan, if he survived ME1 and survived Priority: The Citadel II and did not rejoin Shepard’s crew, will be seen leading a squad of N7 biotics falling back from the transport beam. The squad is wiped out by a blast from a Harbinger. 2.B.ii) Ashley, if she survived ME1 and survived Priority: The Citadel II and did not rejoin Shepard’s crew, will be seen leading a squad of N7 marines falling back from the transport beam. The squad is wiped out by a blast from Harbinger. 2.B.iii) Miranda, if she survived ME2 and Priority: Horizon, will be seen stopping mid-charge. Harbinger’s energy blast blows up a mako in front of her, flipping it over and crushing her. 2.B.iv) Zaeed, if he survived ME2 and was loyal and Citadel: Volus Ambassador was completed, is seen coordinating sniper fire from atop a building. He turns to see Harbinger charge and fire its main weapon at them. 2.B.v) Grunt(and Wrex if he survived ME1), if he survived ME2 and Attican Traverse: Krogan Team, is seen advancing through Reaper troops with a Krogan squad. The team is overwhelmed by the reaper troops. 2.B.vi) Samara, if she survived ME2 and Kallini: Ardat-Yakshi Monastery, is seen with a squad of Asari Commandos fighting a group of Banshees. The Banshees charge in close and impale samara through the chest. 2.B.vii) Shepard’s crew, if they were not taken on the final mission, will be seen behind cover firing on the advancing Reaper troops. The endless wave of reaper troops gradually closes in despite how many are killed. Fade to black as one reaches the squad’s cover. 2.B.viii) More destroyers land near the transport beam and fire upon the remaining “Hammer” forces. 2.B.ix) Hackett listens to the radio transmission that would have been heard during Shepard’s slow motion walk into the transport beam. The “Sword” armada continues its battle as Hackett comes over the radio and announces that the “Hammer” has failed but comments on this being the best shot they will ever have and orders the fleet to continue firing. Some of the fleet will continue fighting and some will flee from the battle(based on the percentage of total fleet war assets acquired). 2.B.x) Joker, if the Thanix cannon and Silaris Armor and Cyclonic Barriers upgrades were not ALL taken in ME2, the Normandy is engaging a reaper dreadnought and is hit by the reaper’s main weapon. The hit does massive damage, the Normandy catches fire and Joker yells as he accelerates and tries to Kamikaze the Reaper but is hit again by the Reaper and the Normandy is destroyed before impact. Fade to black. 2.B.xi) Joker, if the Thanix cannon and Silaris Armor and Cyclonic Barriers upgrades were ALL taken in ME2, the Normandy is engaging a reaper dreadnought and is hit by the reaper’s main weapon. The hit does minor damage, the Normandy continues its strafing run before disengaging. Fade to black. 2.B.xii) Fade from black. A mostly static radio transmission from Hackett is heard stating that “Hammer” has failed, the citadel armada has been crushed, and that their last hope to defeat the Reapers has been lost; the camera fades in to stars and pans over to see the wreckage of the fleet and a comm. buoy before the Reaper surrounded citadel opens up to “birth” a new Reaper Dreadnought from the collected Human population. The message begins to repeat but the screen cuts to black. 2.C) (if Shepard had ≥95% of total fleet based assets were acquired and ≥95% readiness rating was achieved) Hackett listens to the radio transmission that would have been heard during Shepard’s slow motion walk into the transport beam. The “Sword” armada continues its battle as Hackett comes over the radio and announces that the “Hammer” has failed but comments on this being the best shot they will ever have and orders the fleet to continue firing. Some of the fleet will continue fighting and some will flee from the battle(based on the percentage of total fleet war assets acquired).Hackett coordinates fire between the whole “Sword” fleet, focusing the firepower of 1/2 or 1/3 of the fleet on a single reaper at a time. Despite taking their own heavy losses, one by one the Reapers in orbit are destroyed. Some of the “Sword” fleet descends into the atmosphere and assists “Hammer” forces by destroying any remaining destroyers. Fading from black, Hackett is seen standing in front of the Normandy’s memorial wall(Shepard’s name, as well as the names of all of his crew from ME2 and ME3 can be seen on name plaques). After a few moments, Hackett turns and walks into the elevator on deck 3, then immediately out of the elevator on deck 2 before walking up to the CO’s platform, and(camera looking up at him from below the galaxy map) requesting status reports from Joker, Traynor, and the other Admirals before stating “There is a lot of work to do, so let’s get to it.” Cut to image of the Normandy and zoom out to reveal what was left of the fleet, the wreckage of the battle, and the Earth.
3) (if ≥60% of total ground forces war assets were acquired)Story as written at release except that only the destruction option will be available and Shepard will wake up after the scene where the Normandy crashes. Shepard wakes up to see his current squadmates firing at the reaper forces above him(If there were insufficient war assets for Shepard’s squad to survive to this point, two alliance marines would be in their place), before another squad of marines moves forward to cover him/them as they fall back. Dialog takes place with Harbinger talking about the organic’s insignificance and their inevitable ascension are countered by a speech from Shepard regarding the whole of the galaxy fighting together and them never giving up. Shepard(alone or with squad) combats several waves of increasingly difficult reaper forces while using paragon/renegade interrupts to coordinate the remaining “Hammer” forces during the final battle with Harbinger and the other Reaper ground forces. 3.A) (if <60% of total fleet based war assets were acquired) Combat resumes with a comm. message being heard stating that the Crucible has been destroyed by reaper fire during the battle and an inspiring speech from Hackett rallying the fleet to take as many reapers with them as they can. 3.A.i) After the final wave, the camera cuts to the battle in space with the reaper armada annihilating the Sword fleet. The Normandy is seen engaging a reaper dreadnought and is hit by the reaper’s main weapon. The hit does significant damage, the Normandy catches fire and Joker accelerates and tries to Kamikaze the reaper but is hit again and the Normandy is destroyed before impact. Hackett stands silent and resolute on the bridge of his ship, staring forward out the window, the screen jerks back and forth as the ship is shaken by enemy fire, causing one of the consoles behind him to explode. He slowly closes his eyes and the camera cuts to black. 3.A.ii) More dreadnoughts and destroyers descend into the atmosphere, landing near the battlefield. 3.b) (if ≥60% of total fleet based war assets were acquired) Combat resumes with a comm. message from Hackett being heard stating that the Crucible needs more time to get into position. 3.B.i) After the final wave, the Normandy and squadrons of turian and alliance fighters come to “Hammer’s” aid and launch an attack run on Harbinger that damages and distracts it. Anderson comes on the radio and orders Shepard to make a run for the transport beam while Harbinger is distracted. Shepard(and his squad if they are still alive) run past Harbinger and into the Beam, arriving in the Presidium Commons section of the Citadel. 3.B.ii) Making their way past immense piles of dead bodies and keepers organizing and scanning the corpses, the squad works their way to the elevator and up to the council’s audience chamber(unique dialog will be heard in the elevator if any of your current squadmates were also present during the battle of the Citadel in ME1). 3.B.iii) Activating the console triggers the same cutscene from the original ending in which the Citadel arms opening and the Crucible docking. 3.B.iii.a) (if <60% of total Crucible support assets were acquired and 60-80% of the total fleet based war assets were acquired and Shepard sides with Aralekh company in Attican Traverse: Krogan Team or does not complete Attican Traverse: Krogan Team) Electricity arcs across the surface of the Crucible and several small explosions are seen on the outside of the Crucible before it breaks apart and the pieces begin to drift away. The “Sword” armada continues its battle as Hackett comes over the radio and announces that the Crucible has failed but comments on this being the best shot they will ever have and orders the fleet to continue firing. Some of the fleet will continue fighting and some will flee from the battle. Hackett coordinates fire between the whole “Sword” fleet, focusing the firepower of 1/2 or 1/3 of the fleet on a single reaper at a time. Despite taking their own heavy losses(based on the percentage of total fleet war assets acquired), one by one the Reapers in orbit are destroyed. Afterwards, some of the “Sword” fleet descends into the atmosphere to assist the “Hammer” forces by destroying Harbinger and any remaining destroyers, but arrive too late and all of the ground forces have been annihilated. 3.B.iii.a.1) Kaidan, if he survived ME1 and survived Priority: The Citadel II and did not rejoin Shepard’s crew, will be leading a squad of N7 biotics in a charge toward the transport beam. The squad is wiped out by an energy blast from Harbinger. 3.B.iii.a.2) Ashley, if she survived ME1 and survived Priority: The Citadel II and did not rejoin Shepard’s crew, will be leading a squad of N7 marines in a charge toward the transport beam. The squad is wiped out by an energy blast from Harbinger. 3.B.iii.a.3) Miranda, if she survived ME2 and Priority: Horizon, will stop mid-charge. A Reaper Destroyer’s energy blast blows up a mako in front of her, flipping it over and crushing her. 3.B.iii.a.4) Zaeed, if he survived ME2 and was loyal and Citadel: Volus Ambassador was completed, coordinating sniper fire from atop a building. He turns to see a Reaper Destroyer charge and fire its main weapon at them. 3.B.iii.a.5) Grunt(and Wrex if he survived ME1), if he survived ME2 and Attican Traverse: Krogan Team, advancing through reaper troops with Krogan squad. The team is overwhelmed by the reaper troops. 3.B.iii.a.6) Samara, if she survived ME2 and Kallini: Ardat-Yakshi Monastery, with a squad of Asari Commandos fighting a group of Banshees. The Banshees charge in close and impale samara through the chest. 3.B.iii.a.7) Shepard’s crew, if they were not taken on the final mission, will be behind cover firing on the advancing reaper troops. The endless number of reaper troops will be gradually closing in despite how many are killed. Fade to black as one reaches the squad’s cover. 3.B.iii.b) (if <60% of total Crucible support assets were acquired and ≥80% of the total fleet based war assets were acquired and Shepard sides with Aralekh company in Attican Traverse: Krogan Team or does not complete Attican Traverse: Krogan Team) Electricity arcs across the surface of the Crucible and several small explosions are seen on the outside of the Crucible before it breaks apart and the pieces begin to drift away. The “Sword” armada continues its battle as Hackett comes over the radio and announces that the Crucible has failed but comments on this being the best shot they will ever have and orders the fleet to continue firing. Some of the fleet will continue fighting and some will flee from the battle. Hackett coordinates fire between the whole “Sword” fleet, focusing the firepower of 1/2 or 1/3 of the fleet on a single reaper at a time. Despite taking their own heavy losses, one by one the Reapers in orbit are destroyed. Some of the “Sword” fleet descends into the atmosphere and assists “Hammer” forces by destroying Harbinger and any remaining destroyers. 3.B.iii.c) (if <60% of total Crucible support assets were acquired and Shepard killed the Rachni Queen in ME1, and freed the Artificial Queen in Attican Traverse: Krogan Team) The Crucible proceeds to charge up and generates a mass effect field within the torus of the Citadel. The mass effect field intensifies and explodes similarly to the Relay in Arrival, causing a supernova and the destruction of the Crucible, Citadel, reaper armada, “Sword” fleet, Earth and Sol system. 3.B.iii.d) (if <60% of total Crucible support assets were acquired and Shepard freed the Rachni Queen in ME1, and Freed the Rachni Queen in Attican Traverse: Krogan Team)The crucible charges up and releases a number of pulses that extend outward through the system. As the pulses reach the each of the reapers, electricity arcs across their skin and they explode but no other ship in the “Sword” fleet, nor any of the “hammer” forces are affected.
Thus would conclude the climax and falling-action portions of the story. With the resolution to be taken care of through the use of cutscenes like: the debris of the "Sword" fleet in space over Earth as the Citadel "gives birth" to the new reaper harvested from humanity, Hackett staring at the Normandy's memorial wall before heading to the CIC if Shepard and any number of his squadmates die, Shepard and the the whole squad sitting on a beach and staring out at the ocean with a reaper corpse half exposed(which could then become character controlled so that Shepard could go around to each of them and talk about their plans. After this would be a text based epilogue like in Dragon Age: Origins detailing the results of the decisions that were made at a galactic level; such as those involving the rachni, geth, quarians, krogan, etc.
For those of you that noticed I didn't mention what happened to the Illusive Man, he would be the primary antagonist in a post PRIORITY: EARTH dlc that had him elsewhere in the galaxy, still leading Cerberus, but also with a large number of reaper troops under his control.