Note this is very much a "What I would do if I had complete God-like control over the ending" scenario, NOT "What I think Bioware will actually do".
INITIAL POINTS
- Everything until after the mini-Reaper gets destroyed in London is the same. I'm changing the ending here, not the entire game.
- The almost complete omission of Harbinger was (in my humble opinion) utterly criminal. The guy was arguably the main antagonist in ME2, and he doesn't even get a line in ME3. Plus, I want more ham dialogue goddammit.
- The Starchild is gone. Removed. Eradicated. Ceased to be. It is an ex-genocidal baby.
- War Assets become the ONLY determinant of the ending. You spent the whole game acquiring them, may as well use them.
EARTH
- After the destruction of the baby-Reaper, the game continues as per canon with Anderson warning you that Harbinger is coming to prevent you reaching the teleporter. In the first change however, the Normandy is called in to intervene against Harbinger (invent some excuse as to why it has to the be the Normandy and not some other random ship). There are three ways the ensuing cut-scene fight can go (depending on your War Asset score):
Bad Outcome - Harbinger destroys the Normandy, but the distraction allows you, Anderson and your two teammates to fight through the Reaper ground forces and succeed in making a mad dash for the teleporter.
Neutral Outcome - The Normandy is destroyed, but takes Harbinger out with it in an insane suicide run. With Harbinger out of the way, you, Anderson and your two teammates can steadily fight your way through the Reaper ground forces to the teleporter.
Good Outcome - Harbinger is destroyed by the Normandy, which then follows up with strafing runs against the Reaper ground forces. With all resistance eliminated, you, Anderson and your two teammates make their way to the teleporter.
CITADEL
- You, Anderson and your two teammates fight your way through Reaper resistance before eventually reaching the control point for the Catalyst. The final boss battle is against a fully indoctrinated and Reaper-fied Illusive Man (Think Saren on crack, except with no option to get him to suicide). Anderson is shot by you while under the Illusive Man's influence as per canon, and then the fight is on.
- After you've defeated the Illusive Man, before he expires you can either deliver either:
a) A Paragon speech that condemns the Illusive Man for being so arrogant as to think he could control the Reapers and defeat indoctrination, and that all of the humanity that he claims to be working for may suffer the consequences of his hubris.
b) A Renegade speech that condemns the Illusive Man's weakness in allowing his will to be subverted by the Reapers. You state that where he failed, you will succeed to eliminate the Reapers as a threat to humanity and the galaxy.
- Anderson surviving or not is not dependent on your War Asset score, but on how long it takes you to defeat the Illusive Man (think of it as him needing medical attention that you cannot provide while fighting). If Anderson survives, he can direct the battle between the Reapers and Sword fleet personally while you activate the Catalyst. This has roughly the same effect as it does in canon (i.e.: reducing the War Asset score required to get various endings by -1000, the effect of this will come apparent in the next part).
I now shamelessly steal Alesyka's idea about the Crucible being a massive "off" switch for the Reaper's kinetic barriers. This means the ending comes down to a no-holds-barred, do-or-die battle on the ground and in space between the Reapers and everybody else. An extended cut-scene shows the battle in full swing. In space, endless waves of Geth fighters throw themselves at the Reapers to defend the big guns of the Quarian Heavy Fleet, and a boarded Turian dreadnought is saved from the Reapers by a legion of Krogan who smash boarding pods into the ship and, side-by-side with the Turians, clean out the Reapers deck-by-deck. On the ground, ex-Cerberus guinea-pig Jack and Cerberus-cheerleader Miranda fight back-to-back against endless waves of husks and Marauders, cold-blooded mercenary killer Zaeed Massani performs a genuinely selfless act alongside his ex-Blue Sun comrades as they hold back the tide to save a devastated Batarian strikeforce, and the Rachni tear apart their Reapered counterparts with unbound fury (Insert your own scenarios as you see fit, basically the point is to show off the forces you've collected and how you've unified formerly implacable foes against an infinitely greater threat). As the dust settles, your War Asset score ultimately determines the ending...
ENDINGS
In order from worst to best. Harbinger alive guarantees an ending from 1-3, and his death will unlock 4-5. Only with Harbinger dead, Anderson surviving and a large War Asset score (through multi-player only) will the best ending (6) be achievable.
1) The battle is fiercely-fought, to the death, and ultimately futile as the Reapers (even without kinetic barriers) are far too strong for the younger races. As you watch helpless on the Citadel as the Reapers cut the fleet to ribbons and descend back to Earth, Harbinger arrives to mock you personally. "Did you honestly think the cycle could be broken? Every cycle has had its Shepherd. They all failed. You have been no different. Now you will serve us". The last scene is of a Reaper rising above the surface of a clearly-lifeless Earth, with an "N7" logo faintly visible on its pristine surface.
2) The battle rages and appears for a brief period to be in the balance, until the Reapers finally regroup and eradicate the fleet. In the process, the Citadel (and everybody on it) is destroyed in the crossfire. As scenes of the total reaping of Earth follow, Harbinger announces that the length of the termination of this Cycle will probably be several centuries longer than planned, and that the destruction of the Citadel and the unexpected heavy resistance must be taken into account and learnt from.
3) In the course of the battle, the Reaper fleets are driven back and ultimately destroyed at an appalling cost. Earth is a worthless cinder as the Reapers vent their frustration by raising it utterly before being destroyed themselves at the cost of virtually the entire combined fleet, and as Harbinger himself is finally destroyed he plays his trump card. In his death throes, he destroys both the Citadel and the Crucible, and the ensuing wave of uncontrollable power spreads to the Mass Relays, destroying every single one in a galactic-scale chain reaction. The Reapers have been defeated and the cycle ended, but with Earth destroyed, the combined fleet all but annihilated and a new Galactic dark age all but certain because of the destruction of the Mass Relays it is a victory of the most Pyrrhic kind.
4) Shorn of their kinetic barriers and the leadership of Harbinger, and facing down a fleet of races more powerful and numerous than they anticipated the Reapers are destroyed, but take practically the entire combined fleet with them in the process. Only a last ditch defense by the remnants of the combined fleet saves Earth and the Citadel from the death-spasms of the Reapers, and even then the Citadel is so damaged as to be effectively worthless, and large portions of Earth are rendered uninhabitable. You survive and act as a rallying point for the recovery of the galaxy and the Mass Relays remain intact, but with the fleets all but gone, various races (including the Humans, Batarians and Quarians) effectively becoming endangered species, the central government provided by the Citadel erased and most of the homeworlds resembling gigantic funeral pyres any recovery for a disunited, devastated galaxy will take centuries (if it ever recovers at all).
5) The Reapers are destroyed at a heavy (but not catastrophic) cost to the combined fleet, and Earth and the Citadel survive heavily damaged but recoverable. You survive and the Mass Relays remain intact, and all the races of the galaxy pledge to aid each other in the galactic recovery and re-establish the government of the Citadel to represent the interests of all the races, not just the select few. The death toll is astronomical, but the Reapers have been ended and with the races of the galaxy now united the mood is one of tentative optimism for the future.
6) The Reapers are cast asunder by the fury of the combined fleet and utterly eradicated at moderate cost. The Citadel is recovered virtually intact and Earth, while damaged and with a death toll in the billions, will recover in time also. The galactic government is established to represent the interest of all the races, not just the few, and best estimates conclude that it will take mere decades as opposed to centuries for the galaxy to fully recover from the Reaper onslaught. The final scene is of you, Garrus, Joker, EDI and your love interest lying on a beach in Earth, knocking back beers, reflecting on what has happened and deciding what to do next with their lives. The final shot is a pan out to the horizon, showing the flaming wreck of a Reaper in the distance.