Ouch it was confusing... had to read it 3 times. My take (there's a tl;dr at at the end!):
Kuadora (a lil robot built from bacterias from the sea of Enceladus---an ice moon from Saturn) under the guise of Loro, a new student of Calliandra Pandora Girls' Academy (located in Pandora---another moon of Saturn), has been given the order by Neo Nijou (director of Frontier Organisms Saturn Sphere Research Center) to make his little sister Nana Nijou to stop playing truant. As Kuadora was Nana's childhood friend, Neo ordered her to not speak. One day by faking being clueless, Kuadora managed to set up a situation where Nana had no choice but to go to classroom and revealed to be a dark horse genius, which gave rose to a new popularity and helped her with her graduation. During this wave of popularity, other girls all wanted Nana to "coach" them and Nana specified one subject, which was "Dance". (Bonding scene)
After the dance scene, time skipped forward to Nana's graduation day and Nana asked "Loro" if she wants to be free and to come with her. "Loro" however didn't nod and Nana is being called to the ship (which will be departed to Enceladus---where seemingly there will be "suitors" waiting for the girls). After Nana got called up, Loro went to Nana's room and found a letter. Then the scene shifts to Loro running/stumbling maybe trying to catch Nana who just departed. Contents of the letter reveals that Nana knew in the beginning that Loro was Kuadora all along and the fact that Nana was sent to Pandora was actually under her own guise (unlike the other girls who were sold by their families) because she was rebellious against her brother and wanted to get away from his influence, and that Kuadora would be sent there too one day. So the whole scheme is Nana baiting her brother to send Kuadora to her, and to send Kuadora to her hometown, Enceladus (because the whole premise of the school is that all graduates will be sent to do scientific research on Enceladus). After all, we've been revealed from Nana's childhood flashbacks that they were always together until Kuadora was forced to be split up and do work. But in the end Kuadora didn't nod to Nana's request, perhaps because she didn't realized Nana's scheme was to free her. And Nana didn't tell her this was probably because if she told "Loro" that she can be freed and go to her hometown, "Loro" would probably leave her.
At the very last minute when the ship verified that everyone's on board, we've been finally given an insight of Kuadora's head where she was yearning for freedom the whole time. But once she stepped outside of the airlock, there was no ship. And it is revealed the fate of the graduates (who perhaps couldn't find a suitor?) are all discarded, and there was a playback left by the brother who triggered if Kuadora ever goes out of space (the brother predicted that 4 years after "Loro" go to Pandora they will be out in space but Kuadora prolly actually violated this and went away sooner---seeing as Nana was going to graduate in 1 year and "Loro" was only a freshman).
Right away after the message ends weird tube-like "organism" appear and "swallows" the girls. The brother once again prepared this creature ("fed some high quality stuffs") so that he can gather more data of the Saturn Sphere, and orders Kuadora to do it because she is very reliable and trustworthy.
However once Kuadora observed inside the creature, it seems that the girls were actually safe and not harmed at all (it meant that the creature went against his master's---the brother's wishes), and Kuadora realized that she can do the same, "That ends today. I'm quitting this dull job. Let's go for a walk." on the next page "If we find somewhere good along the way, we ca spit them back up". "I won't ever let them catch us again.". This summarizes that both Kuadora and the creatures are collaborating together, trying to find a safe haven from the brother/researcher/saturn sphere to release the girls and they can go and have a dance party again.
tl;dr: Girl went to a school to rebel against her scientist brother and to bait her childhood friend which is being to forced to work as the brother's assistant. However, she doesn't know that the path of not getting married = death. The brother sent the assistant to make his sister walk the right path "get married" to save her from getting eaten to this creature he's been raising. The plan didn't work out. The assistant goes to outer space to find sister & friends safe and that the creature is a good guy. The assistant teams up with the creature to find a new home for themselves and the girls and to get away from the tyranny of a scientist.