I had an idea for Calyrex is this could be when the MC gets kidnapped by all the remnants of the past criminal organizations like Team magma, Aqua, Plasma, and the rest to get the legends he has. Since Calyrex can see into the past, present and future when at full power she would see herself with him eventually so comes up with a plan to round up the remnants of the criminal groups by possessing some of them to come together with their best and WORST who have no morals that if they were to die no one would see that as wrong for what they have done. So Calyrex would not see that part of the future of her getting captured by the group because she gets distracted by her screams of pleasure the MC gives her when they meet. She is highly intelligent that she would solve a problem before it starts by taking care of them all at once especially before they can cause trouble while she is with the MC.
The MC would not be kidnapped till after Eternatus has been dealt with where the MC is going to the poke mart that has been able to reopen and does not have the legends with him to make extra room for things he will buy. He gets knocked out by some sleeping gas and wakes up in a underground base hears Calyrex via telepathy to come to her and free her. Travel can be to open the door by finding a dito that turns into his gear to pry it open, climb down an elevator shaft cables and eventually reach Calrex. The battle would be against all the members but his legends get to him and help him battle which would be a lot of members.