tl;dr sasuke blew up bowsers clown car during 4th wall last year and bowser has held a grudge ever since
the longer version is that sasuke started taking him seriously when something targeting sasuke ended up hurting sora instead, then got spotted by bowser during the tower raid so he ended up having team rocket painting a big target on him
it blew up when tsunade posted and painted a target on everyone associated with sasuke and the ninjas have been paranoid about it, and now they think they had good reason to be because bowser found them by chance at olivine city a few weeks later
after that it doesnt seem like anything big has been happening with that so it looks like whatevers going on is dying down
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the longer version is that sasuke started taking him seriously when something targeting sasuke ended up hurting sora instead, then got spotted by bowser during the tower raid so he ended up having team rocket painting a big target on him
it blew up when tsunade posted and painted a target on everyone associated with sasuke and the ninjas have been paranoid about it, and now they think they had good reason to be because bowser found them by chance at olivine city a few weeks later
after that it doesnt seem like anything big has been happening with that so it looks like whatevers going on is dying down