[This content is out of date and no longer canon (Rafe no longer has any children aside from Sibyl)]
The short answer is that I love drama-filled plotlines and liked the idea of giving Pierce a bunch of lovechildren after chats with @pkmnomegaverse regarding fun drama ideas and this just escalated from that.
The long answer will be under a cut because things might get a tad spicy since it’s relationship drama after all. I’ll also talk about Rafe and his family since it all ties in.
Essentially, here’s how things went. Tory and Bianca (the one from the movie) are happily married and living in LaRousse with their son, Giotto. Rafe is also living in LaRousse, but he’s less happy. Rafe met Tobias by chance at a small-scale tournament while he was travelling in Sinnoh and the two ended up bonding while discussing battling strategies and their encounters with Legendary pokemon. One thing led to another and they end up hooking up and exchanging numbers – Tobias is always travelling around so they could easily meet again if they happened to be near each other. Rafe returns home to Hoenn and eventually decides to settle down in his hometown, beginning work at the Battle Tower helping to referee matches and make sure things run smoothly. He’s also still been occasionally meeting with and hooking up with Tobias over this time period, though he’s also been considering just breaking that off and finding someone to settle down with, since all his friends seem to be doing that.
Unfortunately, things go awry when Rafe unexpectedly ends up pregnant with Tobias’s child, something neither of them were planning for. Rafe does want the kid, but he also doesn’t want to be a single father, so he tries to convince Tobias to settle down with him for their baby’s sake. Tobias, on his part, does try, but ultimately he’s a wanderer at heart, so the situation really just ends up being Rafe as a single father and Tobias being the disappeared dad who shows up occasionally with a souvenir from another region for their son, Azariah, and to “catch up” with Rafe. Since things as they are obviously aren’t exactly satisfying in the love-life department for Rafe, he decides to branch out a bit. He’s pretty sure Tobias isn’t being exclusive when he’s out travelling, so why should Rafe stay exclusive himself? He ends up arranging a sort of friends-with-benefits setup with Tory and Bianca, occasionally joining them for threesomes, which they agree to since they like how it spices up their own love life. Things continue like this for a while, with Tory and Bianca as the happy couple and Rafe making due raising his son and with a not-great but still workable deadbeat boyfriend.
Then Pierce shows up. Pierce, in this AU, has a habit of going a bit wild, both when at the recreated Team Rocket HQ in Johto and when out on missions. He likes having sex with multiple partners, but doesn’t like being committed to anyone, preferring the hookup lifestyle. He also happens to be Tobias’s brother in this AU, though the two are barely in touch with each other. Nonetheless, Pierce is aware that Tobias has a sort-of boyfriend and a kid living in Hoenn, so when he ends up near LaRousse on a mission, he decides to check the situation out. Rafe is definitely surprised to meet Pierce, since he didn’t even know Tobias had a brother, but all the same… Pierce looks an awful lot like Tobias, Rafe is always low-key pining after Tobias, Pierce likes to have fun with hookups on missions, Rafe has regular threesomes with two friends. One thing leads to another, and the end result is Tory and Bianca deciding to have a foursome with Rafe and Pierce. This is definitely a rare chance for something extra different and wild after all. And they all have a good time, Pierce leaves once his mission’s complete and they all go back to their usual lives.
That is until both Rafe and Tory find out they’re expecting. Rafe is… mostly ok with this. He knows the kid is obviously not Tobias’s, but maybe this is a good chance to finally break up with Tobias since things were obviously not working out between them. Having another kid might be nice, let Azariah be a big brother and all. Tory, on the other hand, takes it really badly. He hates the thought that the child might not be Bianca’s. Well, he’d feel better if they were Rafe’s, since at least he’s a friend, but what if the kid is the random criminal’s? This was the worst idea and he can’t believe he thought it would be harmless fun. Bianca is trying to comfort her husband and say she doesn’t mind whatever happens, that the child will be hers no matter what since Tory’s her husband, but it doesn’t do much, especially when Tory finds out he’s having twins. Eventually, once all three babies are born, they’re able to confirm that Rafe’s son is Pierce’s and Tory has one twin that’s Rafe’s and the other is Pierce’s (if Beatrice’s dark blue hair hadn’t made it obvious). Of course, this is a lot to take in for all three parents, but they’re determined to make this work and not let one crazy night mess up their entire futures. Eventually, after he formally breaks up with Tobias, Rafe decides to move himself and his sons in with Tory and Bianca – though just as roommates since even if they’re fwb, he’s not about to come between a married couple in the romantic department. Tory’s from a wealthy family, so his and Bianca’s house is definitely big enough for all seven of them and the kids all grow up together and consider each other siblings. It’s a bit chaotic and a bit of an odd situation, but they all made the best of it and are quite happy by the main fankid era.