Without getting into specifics, the story is set up as a tragedy. The main characters are androids fighting a never ending war against machine invaders and die over the course of the game. You grow to like the characters though, so this naturally makes you feel bad. No matter how many endings you get, they still die.
But when I got the final ending, something interesting happened. While the credits are rolling, the AI helpers your characters utilize throughout the game start talking to each other. With their ward's gone, it was now their duty to erase all data of their existence so that future androids could repeat the cycle. Part of the tragedy is that the fighting is cyclical and pointless.
Before data deletion can begin, one of the AI refuses to comply and states he/it cannot accept this resolution. "You hoped they would live too, didn't you?" The AI gain a sense of self and rebel against their creators by trying to restore the androids' memory from backups. At this point the credits turn into a top down schooter and you have to protect the AI from bullets fired by the credits. In the opening monologue the main character wonders if she will ever get the chance to kill the god that cursed her to her fate, and here you are doing exactly that, shooting the names of all the people who made and are responsible for the game (and by extension, her fate).
This sequence gets harder and harder, until it starts to seem impossible. Every time you die the game asks you if you want to quit. Every time you die, it starts to taunt you more and more with the hopelessness of your situation. Just stop, why waste your time, games are just silly little things, etc etc. And every time you die, a different message appears in the background. A message from another player who has already beaten the game giving you encouragement to continue on. The excellent credits song, originally in Japanese, switches to English.
Eventually you have an entire background of people cheering you on, and then the next time you die you receive a message. Another player wants to help you, do you accept? The soundtrack erupts in a chorus of multiple voices, a half dozen other AI "ships" surrounds your own as you continue to shoot the credits. But this time, whenever you get hit by a bullet, instead of respawning and starting over you continue at the cost of the "data" of another player. Their ship explodes, and you get a message that "Soandso's data has been deleted", before another takes its place.
And then when it's all done, you come out victorious and you receive a cutscene that is easily the closest thing to a happy ending a Yoko Taro game has probably ever had. It's not guaranteed, but at least you have hope now. The AI then talks to the player and asks if you too would like to leave a message for anyone else struggling with the game. You are then told that the person who rescued you did so at the cost of their own save data. You can now choose to make that sacrifice yourself if you so wish.
I'm not sure if words alone can express how exciting and uplifting this entire sequence is. I personally don't really feel any attachment to other people who happen to play the same games as me. But this sequence made you feel like you were all fighting together against the same hopeless (though fictional) fate. It was very powerful, in its way.