In a strange sort of way, the ending. The ghosts that were haunting the animatronics get their revenge on their murderer, and finally find peace.
In a more straightforward sort of way, the good ending. In order to get it, you have to find secrets in all of the minigames around the building that allow you to find the spirits of the dead children and cheer them up by giving them cake. Once you find four, you go to the Puppet's minigame, where all the children you've rescued have gathered around the fifth child, who also gets cheered up with cake. Then the bodies of all the children disappear, leaving behind their animatronic masks, and the balloons above them float up and offscreen, implying that their spirits have finally moved on to the afterlife. You can watch it here.
The implications of this are worth noting for their heartwarming value here: It wasn't killing the Purple Man that saved their spirits. It was being comforted. Killing Purple Man didn't solve the kids' problems; someone being there to show even just a simple, kind gesture does. And that someone is you.
Fans of the Phone Guy can rest at ease. This game shows that he wasn't the murderer! Phone Guy was killed in Night 4 of the original game, while Purple Guy is seen active long after the facility had been shut down and boarded up. Furthermore, Phone Guy was killed by the animatronics, while Purple Guy was able to dismantle them. Lastly, Phone Guy knew just how dangerous the hybrid suits could be, while Purple Guy jumped into Golden Bonnie, and promptly got crushed by the malfunctioning suit.note It should be noted that Purple Guy was panicking, Phone Guy may not have actually died in the Night Four phone call, and there's still a massive amount of evidence that points in his general direction, so it's more less likely as opposed to impossible.
Arguably on the second night, when Phone Dude gives us some archival recordings and we hear that familiar "Hello hello". By now, it's like hearing an old friend's voice again (especially when you didn't really expect to).
This game clears the Puppet's name! Well, to the extent a killer animatronic can be... The child inhabiting it was trying to aid its cause in avenging the murders by causing the other bots to be possessed, and the plan worked! Once the murderer returned and destroyed all of the haunted animatronics, the ghosts were freed and scared the Murderer and chased him into the deadly Springtrap suit. After that, they're free to go. No matter how creepy it was, the first victim managed to turn everything around for all five murdered kids! It's also really heartwarming to think that the true protagonist of the series was one of the murdered children, who totally succeeded in their goal!
There's a running theory that the Phantom Hallucinations are actually the ghosts of the murdered kids trying to save you the only way they know how: by scaring you away from the establishment. They know who their killer is and what happened to him, and they're trying to keep him from doing the same to you.
The Good Ending screen, which can evoke strong emotions. The Bad Ending screen shows the animatronics' heads on the ground with one (or both) of their eyes lit, symbolizing that the children's ghosts are still inside them. The Good Ending shows the animatronics with both of their eyes dimmed, with a just-visible caption saying two simple but powerful words: "the end". Not just the end of the game, but potentially (and most likely) the end of Freddy Fazbear's story that captivated millions and left them sleepless yet hungry for more.
And, given it simply says "the end" instead of "good ending", well, that could mean it's the canon ending.
A subtle one, reminiscent of theories for the first game. This night guard, whoever it is, KNOWS there's something up with the Fazbear animatronics, can probably see the corpse inside Springtrap, and (unlike previous guards) has an easy way to an exit! So why does he stay and keep coming back? Only two real reasons: he's such good friends with the Phone Dude, he's willing to risk his life, or he KNOWS that Springtrap is dangerous and is making sure he can never get out or hurt anyone else.
At the end of the game, the articles surrounding the story of the fire contain bits of trivia relating to the development of the series.
A small one. When you get the Nightmare Mode newspaper, instead of the usual blurred "blah blah blah, you're not going to make it past Night 3" that surrounds the main article, it's trivia about the series◊, like how Foxy was made and how Freddy would only come after you when your power ran out in the first game. Despite it being only a few months since the first game come out, it really feels like the series has grown so much.
It also explains why Foxy's jumpscare in FNAF 1 was so mild. Scott was going to show it to his own kids when he got to see them again. Obviously, he didn't want it to be horrifying enough to scar them, which explains why it was made so mild to begin with.
This song, Balloons, is by MandoPony and takes inspiration from the Happiest Day minigame.