Now, I'm going to start by saying that this is only a possible explanation to the ending, I'm not saying I think this was the best way to end the trilogy. Down to business, then. As we know (those of us who beaten the game) the game ends with the Normandy crash landing on some remote world. I and many others have been asking one simple question to this: Wait, what? At least to me, the events all seemed unconnected. First the Crucible fires, then people cheer, then Joker runs away, then old man talks to child. Confusing, no? But when we think about what happens, it makes a little bit of sense. When the Crucible initially fires, it gives at a pulse that hits the collectors, but it is delayed before the signal is sent to destroy the mass relays. Now, when a mass relay is destroyed, we know what happens: everything in that system dies, that's the whole reason we start on Earth in the first place. How long the delay between ending the reapers and total destruction isn't really given, but I'm going to assume that it give Joker enough time to go down to the surface and see what's up. Once there, the Normandy crew is all reunited on board and everything is happy. And then sensors or EDI or someone notices: there's a giant fireball headed this way. Now, I'm sure many ships, if they knew this was happening tried to flee, but the Normandy was the fastest and it barely was able to escape. So now the entire galaxy is back to page one. The vast majority of the spacefaring races are gone, only disparate colonies that were far from mass relays (which are few and far between) are all that remain as well as the Normandy survivors on some remore planet. After the credits then, we see an old Stargazer telling a child a story about the Shepard, now there are to things I believe can happen here.
1. The old man is Joker, as he is the only consistent character I have seen across the endings. As well, the sky on the planet they crash and the planet with the Stargazer look similar with moons and planets in the sky.
2. The old man is Shepard, seeing that he survives the Citadel. How they found his body in rubble from a crashing space station, when he was already bleeding out, and in time to escape the exploding galaxy is beyond me, but it's possible...
This leaves the question of why the mass relays were destroyed in the first place... Well, the only thing I can figure out is that the Citadel has realized it's solution to chaos is insufficient and that it's technology is now either aiding the chaos (organics) or it is a defense mechanism incase of breach. In the case of singularity (the green ending) the reason it destroys the mass relays is so that the organic-synthate hybrids can now evolve and grow on their own, they are the quintessence of evolution, they don't need help. And that is why Joker franticly flys away. Aaaaand this also leaves the possibility for some sort of sequel. The child at the end could be the child of Shepard and his / her love interest or someone else on the ship (if Shepard was homosexual or abstained from hanky-panky or if it was a she who romanced someone other than Liara). This child could be the next main character. They're growing up in a world void of mass effect technology and they'll be rediscovering the stars.
Anyways, I know many people are not pleased with the way the trilogy ended, but hopefully my speculations can at least allow you to logically see the ending and quell a little bit of the frustration. Hope it helps explain something in a clear way, even if they're all wrong.