Your squad members before the relay don't partake in the final charge, instead staying back with a small group of soldiers and the rest of your crew, including any surviving ME 2 squad members that made it, to hold back a large force of indoctrinated forces that are trying to charge the rear and stop the alliance making it to the beam.
Everything else plays out the same until after the illusive man encounter, after which..these choices happen depending on EMS.
EMS at lowest: The crucible simply doesn't work due to the alliance making it "Far too quickly with too few resources". As Shepard lays half-conscious on the floor of the citadel, Harbinger suddenly flys up into the window and charges a beam. No dialogue, no speech, just him firing a laser as Shepard looks on in horror at the reapers decimating the fleet before being incinerated.
EMS low: The crucible prepares to fire, Shepard looking on satisfied as it does. Unfortunately, whilst it charges warning lights appear on the console speaking of a 'malfunction', making Shepard look on in confusion. Then, it fires...blowing the citadel up as it does. While the resulting blast wipes out the reapers, it also fries earth and everything within the Milky way, destroying the gathered fleet. It then continues spreading out across the relays and too other star systems with the same result.
EMS medium: The crucible prepares to fire, Anderson and Shepard having a conversation about family (Eg. This one, naturally changing depending on gender: http://www.youtube.com/watch?v=CDWpd9nCKws) before they finally die from blood loss. Down below on the ground, the crew you left behind are all overwhelmed and killed as it fires. If you have a L.I, they will look up as the blast comes their way, but end up being killed as the first reapers start to fall from the sky and collapse. They will say some variant of the word "You did it. Y-you actually..did it!"Before they get overwhelmed by the last of the reaper forces and are killed. It then fades out before fading in on a memorial service being given in honor of all that "Gave their lives". In attendance will be everyone you've helped from the main game/side-quests provided they survived (Eg. Conrad Verner) before the coffins of everyone are carried out in typical military fashion, Gun salute included. As the final Coffin is carried out the shot cuts to a memorial with the names of everyone that was at the final fight, zooming in on the name "[First name] Shepard" before finally fading to black and credits.
EMS High: Same as the first, except instead of the crew dying the blast fires just slightly faster, managing to wipe out all the husks and leave the entire crew alive, even EDI (Who naturally makes some manner of comment about this) before everyone starts cheering. It is then that everyone starts cheering in Victory as the reapers start to fall from the sky and die. If you have an LI they will be the only one not cheering, simply looking up at the citadel before making a mad break to the transport beam with a distressed look in their eyes. The other squad members suddenly stop cheering and follow along, moving into the beam. Upon reaching Shepard the LI will suddenly rush over, grabbing their shoulder before saying "Shepard!?". At this point Shepard will look up, simply saying the love interests name before they die of blood loss. At this point the LI will continue to call out Shepards name before hugging them close, letting out a final pained scream before it fades out to the funeral service mentioned above. It is as above only instead, before the final coffin is carried out the LI's hand will gently brush over it as it's carried away. If you have an LI, this ending is achieved regardless of actions in the game.
Variations:
NO LI, Wrex lives: Only difference here is instead of the love interest rushing in, Wrex is the first one to rush in instead. After reaching where Shepard is, the ever popular meme between them is acted out one final time. Wrex grabs Shepards shoulder, simply asking "Shepard.." in concern before Shepard looks at him, saying a weak "Wrex.." before dying of blood loss. Wrex's expression is one of pain but otherwise he just waits their solemnly until the rest of the force arrives. Funeral carries out the same only without hand lingering over coffin.
NO LI, Wrex dead, Genophage cured, Grunt alive: Same with Wrex, only it's Grunt instead who rushes in. Same as above they enact the meme out one more time, as Grunt speaks a concerned "Shepard.." before Shepard replies with a proud, but weak."Grunt.." Shepard will then paraphrase Andersons last words as they slump forward weakly."You did good Grunt, you did good. I'm...proud of you.."Before dying of blood loss. Funeral carries out same as above.
NO LI, Wreave in charge, Genophage sabotaged/cured, Mordin alive, Grunt dead/alive: This time it's Mordin who rushes in during Shepards dying moments, quickly rushing to their side with a shocked "Shepard!" It's then Shepard looks at Mordin, giving a smile before saying to Mordin "You're late.." At this point Mordin will go into one of his usual speeches, exchanging a few mild jokes as Shepard dies, making a comment of being 'out of medi-gel'. The exchange ends with a simple "Thank you Shepard, for opportunity..to do good" at this point Shepard gives a final smile before finally dying of blood loss as the rest of the troops pass through. Funeral carries on as above.
NO LI, Genophage sabotaged, Mordin killed, Wrex was leader and killed, Grunt dead: Ohh boy...this is a sad one. You don't get the speech with anderson this time and the crucible just fires, Anderson simply dying after saying "God, it feels like years since i just..sat down.."After the reapers start dropping from the sky, everyone starts cheering but nobody seems to go to where Shepard is. Shepard briefly checks Anderson, and finding he's dead starts shaking their head and saying they don't intend to 'die in this place alone'. Getting to their feet, they begin to weakly hobble through. Continually trying to hail anyone for a medivac but discovers their comm is out of power. At this point we start to get montages of all the evil choices made: The murder of Wrex, The killing of Mordin, etc as Shepard gradually gets weaker, eventually beginning to hallucinate everybody they've lost and killed (Eg. Anyone major ally character you killed over ME 3 and anyone you lost in the suicide mission). Shepard desperately tries to hail again, receiving only silence before reaching the beam only to find it's shut off. At this point, confronted with the hallucinations, Shepard absolutely breaks down and starts screaming their head off about not wanting to die, saying they have more to live for. If slightly more paragon then renegade, they'll list off their major accomplishments and when they beat the odds but gradually grow less and less confident as time wheres on. The hallucinations just stay silent and stand their staring before Shepard breaks apart, blubbering how they don't want to die before finally dying from blood loss. The last words are "H-how..could it end like this!?". The hallucinations fade and the camera zooms out down the empty corridor, as Shepard lays their alone, dead. More renegade then Paragon loses their head completely and just starts firing on the hallucinations, causing them all to "Die" one by one until, finally shepard is alone."Alone..as usual huh?" Shepard then chuckles cynically, although their is a hint of sadness to it before they elicit a single "Damnit.."Before falling over dead. Same zoom out as above.
Any other conditions: Same as all variations prior to one previous, only it's a group of nameless grunts that find shepard and anderson already dead. Funeral proceeds the same.
Max EMS: Follow the same criteria as above for the previous endings only, instead of finding Shepard dead the LI/Grunt/Wrex/Mordin/soldiers find Shepard barely alive and quickly help them out of the citadel. As they recover in the hospital LI (If Shep had LI) will show up and they'll have a tender moment where they discuss the future, (If Liara cue "Lots of little blue children" line) before they watch the memorial service on holo. If no LI, then it's simply Joker that pops in and shares witty banter. It then cuts too an undisclosed time later where Shepard is decorated for their service and given medals for their service alongside their comrades. During this time Shepard can choose options on making their final speech, choosing to either decline the medals and leave the ceremony with LI + Crew in Tow or just accept the medals and share an embrace with their LI. At this point Joker makes a smart remark about them ordering a wedding cake as the scene fades out to the applause of everyone. If no LI and Shepard declines medals, just show them and crew leaving. If accepted, Joker instead says "So, does this mean we can go party at Afterlife now?"
Variation:
NO LI, Genophage sabotaged, Mordin killed, Wrex was leader and killed, Grunt dead: Happens the same as the last one only, instead the beam is active at the end and after stepping through it Shepard collapses as a squad of soldiers makes their way to help Shepard. It then cuts to an undisclosed amount of time later where Shepard is visited by Admiral Hackett in hospital who says that, now that the war is over Shepard has to face a tribunal over war crimes. Shepard is naturally pissed about this but Hackett responds with Shepard having "Brought it on themselves". Here the paths diverge slightly:
Council Dead: Shepard has the book thrown at them rather brutally but has the option of defending themselves. If they successfully convince the council they manage to get off with just a discharge and a stripping of all awards/medals/Military and SPECTER status. Shepard walks out of the Court-room understandable annoyed and approaches his crew, only for them to just turn their backs and walk away in disgust with Shepard, leaving Shepard utterly alone. If they fail to convince the council, they are declared guilty and escorted away to face "The firing squad". The screen fades out as Shepard is escorted out of the court room.
Council Alive: Same as above. If successful, Shepard is discharged but finds his crew who just give a nod of understanding and walk out of the courtroom with Shepard, all of them seeming to support Shepard. If unsuccessful, Shepard is again faced with firing squad. However, it then cuts to another scene once where Shepard is cuffed and facing a squad of alliance soldiers who prepare to shoot them. It is then numerous explosions are seen and the Normandy is seen flying overhead, with James Vega at the open door at the back calling out to Shepard to jump into the hovering vehicle. Shepard does so despite the alliance soldiers recovering, and manages to make it in just in the nick of time before the door closes and the ship flies away.
As they get out of the planets atmosphere, Shepard is able to talk to Joker and the remaining crew who all admit they couldn't just let Shepard die despite what they did in the war. Shepard has some dialogue choices to say either apologising for making them all fugitives, or saying he's glad they didn't just leave them to rot. The scene ends with Shepard in the cockpit with Joker and Edi with Edi making a comment about them "No longer being pursued" leading Joker to ask Shepard "Where too now Commander?"
It's at this moment the rest of the crew walks up into the cockpit behind Shepard with Shepard just smiling before saying."Anywhere. It's a big universe out there...let's see what else it's got to challenge us with" The rest of the crew make various comments but all of them agree to staying with Shepard. It's at this point Shepard says "Joker, Punch it!" With joker and Edi both replying with "Ai ai Commander!" Before the Normandy enters a relay and is propelled off, the scene ending on a shot of the relay once Shepard and Co pass through it, eventually fading to black and credits.