First, EMS determines what happens during the beam-rush, when Harbinger comes down and starts blasting everyone.
- With very low EMS, you get the failure ending. Harbinger kills everyone (and blows Joker out of the sky when he comes in for support). He talks to you personally to gloat that you've lost, then lasers you to death. Reapers win, destroy the fleets, spend the next century reaping the galaxy unchallenged.
- With merely low EMS, Harbinger blows up *most* people. You're the only survivor to reach the beam.
- With medium EMS, you and Anderson survive to reach the beam, but your party still dies.
- With high EMS, you and Anderson make it to the beam. Your party survives, and stays on the ground to defend the beam against husks that might try to follow you up.
From there, the ending is the same as what we got, up until the point that TIM is dead, and you and Anderson (if you had enough EMS to get him up there with you) are talking and he dies. If you have very high EMS, Anderson's conversation is about twice as long, and much more heart-wrenching. See the audio here.
You try to activate the Crucible, Hackett says its not working. Harbinger speaks through the dying TIM, telling you you've failed and that he's got your friends in his cross-hairs. He shows you an image of Joker loading up the parts of your party that survived.
Harbinger demands that you submit to him. He claims that he is impressed with humanity and will have the Reapers spare your race and your squad if you do so (but still reap the rest of the galaxy). If you press him for information, you learn that the reason for reaping is largely fear of rivals getting too powerful, but they've convinced themselves it's for our own good to be remade into Reapers like them as well.
You can submit to him, getting the second ending. The Reaper fleet spares Earth, but wins the overall war and reaps the rest of the galaxy.
If you challenge him, and your EMS is low, he kills your entire squad. If it's high he still attacks, but only some of your party may die, depending on choices you've made.
He activates the lift to take you to the area with the three options, explaining that a new solution may be needed. (No Citadel-Child here! Yay!) He originally only gives you the Synthesis option, which saves his kind. This is the third ending. It's basically the same as the Synthesis ending we actually got.
If you have a high enough reputation, you can challenge him again and open up the Control and Destroy options. He acknowledges that Shepard may present a perspective he hadn't considered, and so the Control option makes the Reapers leave, at least for now. This is the fourth ending. The Reaper fleet lifts off and simply goes away. Everyone is happy they've "won", but uneasy about what the future may hold since the Reapers may return some day.
Finally, since you're in control of the damn machine, you can just do Destroy. Harbinger explains that doing so will kill the Geth and blow up the relays, too (and he's telling the truth). This is the fifth ending. After blowing things up, you're beamed back down to Earth and found by your squad. Everyone celebrates, but it's a pyrrhic victory with the relays gone.
This, all together, is a *much* better ending. Every ending is distinct, the order you're presented them makes sense, the Reapers have a believable reason for reaping, and it's just altogether ridiculously more coherent.