On 6 June 2003, Thomas was released from Pakistani custody, at which point he was deported to Australia. He spent nearly a year and a half subsequently living with his family in the Melbourne suburb of Werribee, Victoria, before he was arrested by the AFP on 18 November 2004 and charged with several federal offences, including one count of possessing a false passport (an offence under the "Passports Act 1938"), and one count of receiving funds from a terrorist organisation and two counts of providing resources to a terrorist organisation (offences under the "Criminal Code Act 1995").