John Sullivan was indicted on July 6, 2006, when the Drug Enforcement Administration executed massive simultaneous raids on half of San Diego’s 19 medical marijuana dispensaries. The action shut down most of the dispensaries in the region, including Sullivan’s “Purple Bud Room” and “Tender Holistics Care.”  During the investigation of these facilities, which began in September 2005, an undercover officer claimed that he was able to purchase marijuana for his dog.

These raids were a follow up to similar raids in December 2005, where thirteen dispensaries were raided by the DEA, SDPD, and the San Diego Sheriff. At both times, police confiscated medical marijuana, money, patient and financial records, computers and cultivation equipment. In the July 2006 raid, however, police arrested at least ten people on state charges and six people on federal charges. The federal defendants included Wayne Hudson, Christopher Larkin, Ross McManus, Scott Wright, Michael Ragin, John Sullivan, who were all charged with conspiracy to manufacture and distribute marijuana. Sullivan had the additional charge of manufacturing marijuana. Hudson, Larkin and McManus are former operators of the "Co-op San Diego" dispensary, while Sullivan operated the "Purple Bud Room" dispensary.

Co-op San Diego defendant Wayne Hudson was sentenced to 1 year in prison, plus an addition four years of supervised release.  On February 26, 2007, defendants Larkin, McManus, Wright and Ragin were sentenced to five years probation.

Sullivan’s indictment contained counts for cultivation, as well as for conspiracy to cultivate and conspiracy to distribute marijuana. While also facing state charges stemming from the raids, Sullivan pled guilty in federal court to growing three hundred marijuana plants. In August 2007, he was sentenced to five years in federal prison and five years of probation. Sullivan served some of his time in Oregon, before being transferred to a federal prison in Florida.