Well the main difference between the two is that in this story there's humans and gijinkas, but in the original it was just fusemon. It opened up with them being produced in a factory, with the main character (Shaylava) waking up to consciousness. She notices immediately that no one else seems to be aware, their eyes glazed over. Then the instant she spots someone that has clear eyes, that individual is incinerated. Shaylava freaks out mentally then realizes she's about to pass the check point that individual got incinerated at. She freezes and tries to pass as a mindless individual. By some miracle, she gets through and is sent to one of the three sections of the laboratory. If I remember correct she got sent to the "Fighting" section or something like that but it's been several years since this story. So she goes a day living here only to be cornered by another fusemon, Dewfezant. He says she's not playing the whole mindless individual very well and offers to teach her. They begin to work together and soon their supervisor, Unpunny, sends them to the next area, the Survival Area. Here they learn how to survival in the wild and whatnot, Shaylava being a natural at this area. There they meet two other fusemon that aren't mindless, Vulveeon and Cyndamin. After about two weeks they plan to move on again when their supervisor, Haxozard, requests that Shaylava stay behind so that she can be his successor. Unpunny and the head of the facility agree, so the group must move on without her. Shaylava trains separate from everyone else from then on, and after what seems like months they "awaken" her (even though she's technically already awake). However, soon after this happens there's an explosion in the next area over, the Intelligence area (I think). During the time Shaylava was training, Dewfezant, Cyndamin, and Vulveeon met two other awake fusemon, Quillmin and Umbretails. They ended up sabotaging an experiment set up by their supervisor, Shikachu. They ended up trying to flee the facility but are stopped by the three supervisors and Haxozard orders Shaylava to kill the rogues. When she refuses they realize she is one of them and send them all to the dungeons below the building. There they meet the man in charge, Mewthree. He explains the whole reason he founded Tri-Kappa Labs was to stabilize his form since prior to the founding it was quite erotic. After injecting the DNA of every Pokemon into him, he stabilized and became the ultimate being. Then he created an army of fusions to take over the world, you know the usual villain stuff. The group vows to defeat him, he tells them they're too late, then leaves. They try to escape but there's no way out. Everyone except Shaylava becomes depressed earning a pep talk from Shaylava. They ended up escaping (I can't remember how but it had something to do with explosions). Alarms start blaring and they try to make their escape. The supervisors try to stop them but end up joining them as the whole place collapses. In the midst of it all, Mewthree says he's not going down alone and uses psychic to prevent Unpunny, Haxozard, Shikachu, Dewfezant, Vulveeon, and Umbretails from leaving. They whole place collapses down on them and only Shaylava, Quillmin, and Cyndamin make it out alive. The epilogue skipped almost a decade into the future where the place had become a sanctuary for fusemon with the only living three main characters acting as guardians. Shaylava and Quillmin had a kid they named Citrus, he was a Shayquil because he looked very different from Cyndamin. The epilogue gives a description of the place and how much it changed from Shaylava's perspective. She reminiscences about the days ten years prior and breaks down into tears. The story ends with her looking out over a nearby lake and seeing something in the water's reflection. She looks up just in time to see a familiar figure, Mewthree, soaring in the sky just before he jumps into a portal.

There was supposed to be a sequel titled Beyond the Sanctuary where Shaylava, Quillmin, Cyndamin, and Citrus all leave the sanctuary in pursuit of Mewthree. I actually found a few notes on this mentioning that they would travel across a region called Ascater. The whole place had anti-fusemon laws so it's hard for the group to navigate around but the reason they have these laws is because Mewthree has taken over the Champion's mind. The group ends up going to the Champion and he battles them using the mind controlled versions of Dewfezant, Umbretails, Vulveeon, Shikachu, Unpunny, and Haxozard. They end up defeating the Champion and having to face Mewthree. They defeat him but only after snapping out their friends and the whole group attacking as one. They defeat Mewthree once and for all then head back to the Sanctuary to continue as guardians of the place.