Random Access Memories
As you'd expect from the conclusion to an epic trilogy, a ton of stuff goes down at the end of Allegiant. Basically the entire Bureau of Genetic Welfare is brainwashed into forgetting the whole "genetically damaged" thing. Tobias convinces Evelyn to give up control of Chicago in exchange for world peace—or at least regional peace. And (spoiler alert!) last but not least, our main character croaks.
We go over the specifics of Tris's death on her character page (take a few tissues with you, just in case), so we'll talk about the other two things here.
The entire plot of Allegiant revolves around figuring out what's outside of Chicago. The answer: the Bureau of Genetic Welfare. It's revealed that Chicago is a giant social experiment (like The Real World times a million), and that it's going downhill faster than that show did when it moved to Las Vegas.
The Bureau decides to brainwash everyone inside of Chicago using a memory serum. Tris and her friends do not want this to happen (obviously), because that's pretty much the same as just murdering everyone.
So Tris ends up doing the exact same thing to the Bureau. She unleashes the memory serum on them, after inoculating all her friends. Isn't that a bit hypocritical of her? Was her plan any different from Nita's, which was to just kill everyone in charge?
Another plot that has been going on since Divergent is the power struggle for the city. From Jeanine to Marcus to Johanna to Evelyn, adults have been battling for control of the city for chapters and chapters and chapters.
The sticking point in the battle for the city has always been the faction system. Some people want factions, some people don't. The problem is that the factionless are pretty much just another faction, intended to limit people's free will and impose a system of control on them.
Tobias finally manages to talk sense into Evelyn, his mother, who is the leader of the factionless. It's about time someone managed to say what we've been thinking this whole time: "The reason the factions were evil is because there was no way out of them," [Tobias] say[s]. "They gave us the illusion of choice without actually giving us a choice. That's the same thing you're doing here, by abolishing them. You're saying, go make choices. But make sure they aren't factions or I'll grind you to bits!" (48.39).
After Tobias says this, he begs Evelyn to choose him instead of the city. He's pretty much begging her to act like a mother for once. And… she does. She gives up control of the city and agrees to an alliance with the Allegiant, and everyone pretty much lives in peace. Um, this is sweet and all (try not to get teary eyed during their mother-son hug fest) but why did she come to this decision now instead of years ago, when dozens of lives could have been spared?