Xemnas and Kairi were always enemies. The organization needed Sora to destroy a lot of heartless so he kidnapped her in order to fuel his anger. Xemnas holds Kairi captive in a cell in the Castle that Never Was and lies to Sora when he demands to know her location. She is eventually saved by Riku and Naminé. Kairi helps fight against the heartless that Xemnas summons. He later causes her and Mickey to be separated from the rest of the group when the rest fight against him.
XemKai has a decent amount of popularity in the fandom despite the fact that the two are enemies. Kairi is commonly shipped with members of Organization XIII and Xemnas is surprisingly one of the more popular choices. Some feel that the two balance each other well with Kairi being a princess of heart and Xemnas being a nobody who controls nothingness. He later had her captured which is sometimes a component of enemy ships.