(Spoilers ahead) Once you, the protagonist, reach the planetarium, you meet this girl robot who talks a lot and insists in giving you a bouquet of junk. I like to refer to the protagonist as Mr. Customer instead of Junker, as that's how Yumemi refers to you. In any case, Planetarian spends a considerable amount of time explaining what has happened to the world and how desolate it is.
The Rain is a third character, even. It's more important than whatever else. The war doesn't matter; the destruction doesn't matter; the booby trap that killed the protagonist's partner doesn't matter - but the fact that there's an ever-present downpour is very much stressed by the artwork and the text. What is the Rain like? It (or she, since "rain" is a feminine noun in Portuguese and I can't help but think of a rain as a feminine entity) is negative. Inexorably, unchangeably, untouchably so. She will not stop, she will not break, she will not waver. However, Mr. Customer learned how to live with her.
So you, the player, transit between two worlds: the barren outside, reigned by the Rain, and the barren inside of the planetarium, reigned by Yumemi. She knows every inch of the building. She's a robot, responsible for the planetarium. And what is she like? She is positive. Inexorably, unchangeably, untouchably so. She is a robot, programmed to be like this, yet "just a little broken". She cannot stop, she cannot break, she cannot waver. However, Mr. Customer learned how to live with her.
What is the relationship between these two characters? None. They are completely unaware of one another and the protagonist is the bridge. It is confusing for Mr. Customer and it is confusing for you. The fact that you are the 2,500,000th customer (or, rather, the 2,497,290th customer, or rather rather, 2,497,288th visitor I think) is the whole reason why the story unfolds. She is not a human, there are never second intentions to what she says. She is what she is. She is the same as the Rain - they are two entities that can't ever touch because they are inexorable and will not, by essence and definition, change how they think and what they do.
This is why Yumemi's fate is predictable. The moment she and the Rain clash, Yumemi will die - actually, she cannot die. She cannot feel pain and even says so when a robot blasts her into pieces. She is not a human. This is rather obvious once you think about it. It's a very teleological story - because of these essences and definitions, there is absolutely no other way the story could happen. There was never a possible happy ending. You were a bystander in this encounter.
On the other hand, since you are the bridge, you are responsible for her demise. After all - and this is also obvious once you retrace the story - if you weren't there, Miss Jena would never be fixed, the glorious and beautiful presentation would never happen and the energy supply wouldn't overload. And then you wouldn't have to leave the building with her. The extremes only happen to meet because the protagonist enforced this meeting.
But how wouldn't he? It's also the only thing he could do. And it's what you would do, too. You could easily think, by the way Yumemi acts, that she is a human in disguise, but remember - she isn't. She is a "kinda broken robot", but this is probably enough for us to relate so much to her that it doesn't matter that she can't feel pain. We feel pain in her behalf. She talks way too much and we listen. Mr. Customer listens. Even though - no, since Yumemi is inexorably positive, there is nothing we can do but to bring her to that which is inexorably negative - the Rain.
And of course we, as readers, can do nothing about it. There is a small but very important dissonance between you and Mr. Customer here. Even though Mr. Customer knows all about the Rain and has put up with her since birth, we don't. We just know she is everything Yumemi isn't. Yumemi is upbeat, bright, fun to listen to and a little broken. She thinks of the Rain as "an unfortunate weather", day by day. The Rain will, someday, consume Yumemi, but not even the Rain herself knows that. The energy supply that lasts for one week each year might as well never run out and Yumemi could hibernate forever, but that only matters once we are there. We, the players with no agency whatsoever. Our presence as someone who witnesses this contrast is even more important emotionally than Mr. Customer's presence as someone who fixes Miss Jena. This is why we relate to Yumemi and can't help but think of her as a human, as someone we'd like to hug and take somewhere else - to the Heaven of Robots, if you want.