Out of Universe Reason Edit
Kes was asked to leave, her roll was not progressing the way they wanted and the show was also suffering at the time. Jeri Ryan was brought in to revive the show and they felt that both rolls were not necessary. Personally I thought they could have used Jennifer in a smaller roll as a Alissa on next gen as a nurse.
In Universe Reason Edit
Kes left Voyager after the Species 8472-Borg war after they communicated with her and probed her memories. That increased her telepathic abilities and gave her telekinesis. She was able to do precise movements with tools using only her mind. She started to fall apart at the subatomic level in a transcending sort of way and started to cause serious damage to Voyager. She left in shuttle and became completely incorporeal with extremely powerful abilities. She was then able to propel Voyager closer to home by 9,500 light years.
She left because she became incorporeal. She helped save Ocampa in the novels.