Shepard has a dialogue with the godchild, with renegade/paragon options to reject all of his choices, and see through his deception. Upon realising that the deception isn't going to work, and Shephard refuses to be indoctrinated, we suddenly find Shephard inside an indoctrination chamber together with Anderson (The Godchild thing was just an indoctrination sequence). Shephard frees him/her self with a bit of violence, and now has to take on a Giant reaper hidden within the Citadel. Depending on your choices, Anderson may or may not have been indoctrinated, and might help you or you'll be forced to kill him yourself.
The battle seems futile, until the Normandy comes to Shephards aid and blasts a hole in the Citadel. The player must now make use of his full team, and hand out orders to every crew member. Much like ME2's ending, this is where crew members can die if they are not loyal, or if the player simply picks the wrong person for the job. The player also selects his squad, which ends up fighting the reaper in an epic end battle.
The player might have other squads at his disposal as well during this battle, like the Geth, Ragni, etc. Depending how you handled all the side stories in ME3, your final battle might look slightly different (just like with the finale of Dragon Age 1).
Shephard may or may not still die at the end, but regardless, the universe is saved, and none of the Mass Relays are destroyed. We see an epilogue of what happens to the other races and the other crew mates. No ending of Joker and Edi landing on a random planet for no reason what so ever.