John went to the Caliban Cove mission along with his other S.T.A.R.S. Exeter Branch teammates and fellow Raccoon S.T.A.R.S. Bravo Team lone survivor, Rebecca Chambers. John was shot in the lower back by his former best friend Steve Lopez, who was in control of Dr. Nicolas Griffith's newly created viral substance derived from the t-Virus, that turned the infected into Tri-squads (controlled zombies).
Despite being shot and wounded, John's wound was not fatal, and he survived the Caliban Cove incident along with Rebecca and Captain David Trapp. He then decides to join the Utah operation with Rebecca, David, Leon Kennedy, and Claire Redfield.