In Turn, Turn, Turn (S1E17)
Skye writes all the secret information on the Bus to a disk and deletes the originals to keep it from falling into enemy hands. She then gives the disk to Ward for safekeeping because she hasn't been trained to withstand torture.
Later in the episode,
Ward is shown to kill Agent Hand, and release Garrett who is apparently the Clairvoyant, presumably making him either an agent of Hydra or under their control.
At the end of the episode does Agent Ward still have the disk?