Tom and Daisy leave in Chapter IX because they have no reason to stay. They left town shortly after Tom had revealed the source of Gatsby's fortune to Daisy during the big blow up in New York City. Nick had seen the couple, that same night, sharing a late meal and possessing "an unmistakable air of natural intimacy," despite the fact that Daisy had earlier referred to her husband as someone who "disgust[s] [her]." It seems that Daisy realizes that she can never have the same life, the same status, that she enjoys with Tom if she were with Gatsby instead, and so she simply leaves with her family as if to put the whole dream behind her.
Perhaps she and Tom decide that a trip far from home with be good for them all. They seem to have been happy on their honeymoon, and so maybe they think another trip will help their relationship. He still believes, as far as we know, that Gatsby killed Myrtle, Tom's mistress, with his car, and Daisy seems content to let Gatsby continue to take the blame for that accident. There is nothing to keep them in East Egg, or even New York, for now, so why not take a trip and put the whole ugly business behind them?
After Nick runs into Tom some months later, he describes the couple as "careless people [...] -- they smashed up things and creatures and then retreated back into their money or their vast carelessness, or whatever it was that kept them together [...]." Tom and Daisy do not have to clean up their messes; they do not have to take responsibility. They can simply wash their hands of those individuals who are beneath them, and this is precisely what they do.
There could be many reasons for why they left, I feel that they leave to not have to face the reality of their actions. In the beginning of the novel we learn from Nick that in the end Gatsby was the one that stood out as the 'best'in his eyes and at the end of the novel Nick tells Gatsby that he is better than all of the them put together. Gatsby signifies the hope that the dream is eternal. whilst Tom and Daisy only destroy dreams, they do not care enough to stay and face the consequences of their actions. Destroy and move, that way you do not see the wreckage.