What scenario takes place?
1.
Z-ARC reprograms the parasites in the girls after one gets into Yuya's head and is destroyed. The girls go from slaves of The Doctor, to fanatical lovers of Yuya. Z-ARC then sends the parasites and cards that the girls and Yuya didn't have in the past back to the first season. The parasites replace the girls' minds, thus, no fighting back like Lulu did in the fight between her parasite and Shay.
The parasites have the memories that the girls had when they arrived, and the memories of what they did in control of the girls, but none of their other memories (So, for example, the new Celina wouldn't have the memories of her time as part of the Lancers, other than the memories the parasite pulled up before going back). The girls, being parasites combined with the girls' brains already, are immune to other parasites and can't be taken control of by others.
The parasite girls are in love with Yuya, but that doesn't mean they are his slaves, and can act against his wishes, although they will act for his sake. They can make new parasites loyal to them, and will seek to use them to make slave girls for their harem, with the four of them being equal as queens for the harem. They obviously won't tell Yuya, since he'd object, and they know it. The girls will be very forward in their feelings, and pursuing Yuya.
2.
When Ray split Z-ARC, all of his previous good side was put in Yuya, while his insane self was split between the other boys. The boys will still have their general personalities due to how they are raised, but Yuya won't go 'Berserk Mode,' and the other boys are more likely to succumb to Z-ARC's darkness. Yuya can absorb the other boys, and purify their darkness, but unlike canon, they won't exist in his mind as individual people, he'd just have their memories.
In this story, Z-ARC and Ray were friends, who were in love, but didn't know the other felt the same way, but her father kept her away, and he tricked Z-ARC into thinking she wanted nothing to do with him, causing Z-ARC to feel abandoned and betrayed, and thus, give in to the demands of the crowd to be more violent and destructive, so that they won't just abandon him too, since he was originally shown horrified when he hurt someone badly by accident, until the crowd cheered.
During Yuya's duel with The Sledgehammer, once he gains the Pendulum Cards, he will regain his memories of his time as Z-ARC, and seek to make up for what he did, telling Zuzu, who doesn't remember her time as Ray, but something inside her tells her he telling the truth about their past, and she continues to support him, wanting to make up for what happened, and be open with her feelings so that he knows he's not alone. All the girls love Yuya, as the sole fragment of Z-ARC to be the man their past self loved, rather than an insane monster.
3.
All the bracelet girls, after Yuri captures Lulu and Rin, end up warped into the Standard Dimension, and meet Yuya and Zuzu. All three eventually realize they've fallen in love with Yuya, and Zuzu steps up her game and becomes honest with herself to avoid losing him, before they eventually agree to share him.