So, after the recap of Noriko's actions and the first scene, Saya as the Black Pregnant Angel swoops down to handily defeat both Lenata and Yujika, stripping them of their suits and impregnating them with Homunculus eggs. When it begins to look like Noriko is going to need saving from her savior, who else but Angela comes to the rescue! He says he's coming by due to having some business to take care of, and tells Noriko to take everyone (Lenata and Yujika included) back to Cafe Angela with her warping. The antagonists are brought to the treatment room.
The plot of this game begins when Angela begins his monologue by apologizing for perhaps being the cause of all the incidents relating to PA. See, Angela is actually from a far away planet on which a species of life similar to humans (though all hermaphrodites) lived and constantly waged a war whose origins had already been forgotten. However, a sudden cease fire was declared due to it being discovered that their combat armor, aptly named Protective Armor, carried with it the side-effect of rendering the wearer sexually infertile after prolonged use; they would then only become able to reproduce through cloning themselves or creating homunculi. It was recognized that the threat of their species wiping itself out was greater than continuing the war, and a declaration was made to end it and prohibit future acts of bloodshed. A plan was then drawn up to send out the few fertile members of their race to other planets and have them mate with the species similar to themselves, thereby gradually restoring sexual reproduction functionality to their own kind. Angela, obviously, ended up finding Earth.
At this point, we switch to Ikuma's side of the story. At the time, she was a university researcher whose work had only just started yet already was encountering a major problem. Angela made contact with Ikuma, and asked if she would be able to help her. Ikuma was more curious than suspicious of this lewdly-dressed alien, and her curiosity was all the more piqued when she saw a potential for a break-through in her research in Angela's story. She therefore agrees to help Angela reproduce on the condition that she can study her technology. After many attempts at procreation, Angela is finally able to impregnate Ikuma after using her suit to change the composition of her semen slightly; however, what Ikuma gives birth two are homunculi: the Angela that runs the cafe and his clone. The cafe was made to be the original Angela's home base, and underneath it is her spaceship. Afterwards, Ikuma withdrew from the university and joined Muraki's organization to further her research (which also happened to be carrying out similar research on the aliens’ technology, unbeknownst to Ikuma).
This whole series' backstory now over, we return to the current events. When asked about the suit Saya has on, the Angela homunculus tells the protagonist that that suit is the original Angela's, dubbed "Pregnant Angel Angela." Mimi asks what the difference between an original suit and their reproductions is. Angela states that: the reproduction PAs have limited combat capabilities, especially where special abilities are concerned; the original suits have very strict protocols to limit who can use them as well. Noriko, however, has the potential to use the reproduction suits to their full potential due to her preventing the PA systems from functioning properly.
The knowledge bombs don't stop there, though. After the group is told about Saya, Mimi then shares that she heard she's not actually Muraki's biological daughter, but an adopted one. Angela one-ups her by revealing that Saya is not even an Earthling, but a clone of one of Angela's kind that Muraki's organization made through their research. However, she's imperfect and lacks the original's memories.
After all these reveals, we see Saya using her semen to transform homunculi into clones of herself. Angela declares that she needs to be stopped, and to do so, the Swallow S core and Bunny B suit will be needed. They will destroy PA Angela's core by having Noriko use her powers to smash Swallow S's core into it. (PA cores, by the way, move from the ring to the uterus after transforming.) After our intrepid heroes departure, more anomalous homunculi appear, this time due to being birthed by Lenata and Yujika. Angela takes action to contain them, and Hitoka escapes to let Noriko and the others know what happened personally, since communication is down.
After fighting their way through the crowds of incredibly weak Homunculi S, Noriko and the gang confront the rampaging Saya. Their plan to defeat her fails, because Saya has equipped two more cores from the defeated Yujika and Lenata. Mimi and Ikuma give up their cores to Noriko, then go distract the Homunculi S with their bodies. When the last shot misses and all hope seems lost, it is again Angela to the rescue. He tells Noriko that the only option left to them, now that they're down to just her PA core, is to unleash Bunny B's full potential by releasing the restraints on it. Noriko accepts after some convincing, despite the risk of her also going berserk and having to fight her best friend. She transforms, and goes berserk... libido-wise, that is. She defeats Saya, but still cannot bring herself to harm her. But she then puts two and two together and comes to the realization that her semen, upon being shot onto a PA core, has the ability to strip it of the control functionality a user has. She pounces on Saya and inserts herself, but Saya manages to get inside Noriko too, and they mutually strip each other of their PA suits.
We then fast forward to 10 months later. Cafe Angela is gone, and Noriko is visiting the site where it once was to reminisce and meet up with her friends and former enemies. In the aftermath of the Homunculi S outbreak, everyone who was raped by them (both men and women) have now gotten pregnant due to the light released when the A and B cores were released and fused together; Angela took this newly-formed core back to his home planet, declaring that it should be what’s needed to solve its woes. Ikuma is able to profit off of T Town’s pregnancy epidemic after she perfects her PA design and creates the “Simplicity PA.”
Suddenly, a new PA appears, and it’s Muraki. Or rather, it’s a PA inhabited by Muraki, who moved his spirit into it just before his body was destroyed and had his team finish it through using the technology of Angela’s people. He madly declares that he will surpass Ikuma and commands the Noriko clone wearing the PA Zero suit to destroy the protagonists. Yet another PA appears suddenly, but this one is an ally. It’s Angela, in her new and still-developing clone body. She returned by herself upon realizing that not all the cores had been collected and accounted for; Hitoka and the ship are still on course for her home planet. To help in the fight, Angela gives Noriko and Saya reproduction suits of her PA Fafnir. She states that though the suits do not have limits placed on them, because they’re made from the cores which they gave birth to, the chances of them rampaging should be low. Thus, the game ends with the trio leaping into combat.
