Well, that ending was bullshit.
I don't know, maybe if I understood the plot more (I can't help but feel that I have a real comprehension problem with all these video games that I can barely follow), but from what I gather, the game is set in a kind of virtual world where people live their whole lives, it's slowly being destroyed by an aggressive reformatting program, and your sword, the titular "transistor" is an important memory stick/programming dongle that can store the personalities of dead people (who may be real people connected to the city or perhaps they are programs who exist inside the city itself), and you have to track down the conspiracy of wealthy citizens who triggered the apocalypse out of a misguided attempt to "improve" their world.
But if that's the plot, then the ending is impossibly bleak. The main character, Red, gains the power to restore the city of Cloudbank to its former state, but she finds that she is unable to bring her loved one, the voice from inside the transistor, back from the dead. Presumably, this means that all the other people who died during "the Process" are gone forever as well, and thus rather than live alone in an empty world, she commits suicide. Dark.
I'm not an especially spiritual person, so the argument that this is a happy ending because they're together in heaven (as shown by a beautiful picture shown behind the credits) doesn't find much purchase with me. I suppose it could be digital heaven, and that by stabbing herself with the transistor, Red was merely uploading her consciousness into it, so that her and her boyfriend could persist as mind-states in another level of the simulation. But if so, that's the sort of thing I'd prefer to have spelled out.
Or maybe I'm being too hard on the game. The story is really only the barest wisp of a thing. Most of the game's power is in it's atmosphere and mood. Everything about it, from the soundtrack to the voice acting to the color palette is dripping with melancholy. Transistor is a game about loneliness. You are in an empty city without a voice of your own, because it was stolen by the villains, people of immense power who nonetheless don't know what they want, just that they can't find peace in an ever-changing world shaped by the fleeting desires of the teeming multitudes. The world is doomed because the elite don't have it in them to find authenticity inside themselves. It's probably telling that heaven/the simulated world inside the transistor is a pastoral countryside whose bright colors contrast the decaying city.
It's probably still bullshit, though. The villains don't trust democracy and the hero is happier in the country, but you have to view both in the context of a dead world, where none of that really matters all that much. I liked Cloudbank, and though I only knew its citizens through snippets of news reports and brief unlockable biographies, they seemed like neat people. It bums me out that they're all dead, and no amount of frolicking in the sunshine is going to cheer me up about it.
Still, I liked playing the game. I especially enjoyed the challenge levels, where they give you a predetermined weapon loadout and a goal, and let you have at it. I'm not sure what the conditions are for opening up new challenges, but I still have about a half-dozen to go, so I'll likely enjoy my new game+ immensely. And who knows, maybe I'll see something on my second playthrough that will change how I feel about the story.