In September of 1996, he encountered LAPD detective Harry Bosch while Bosch visited Las Vegas to investigate the murder of Anthony Aliso. Bosch was looking for Aliso's girlfriend Layla who had been a dancer at Dolly's. Flanagan tried to get tough with Bosch, but Bosch beat up Flanagan.
A few days later, Flanagan was at the safehouse where Eleanor Wish was being kept. Tom and Jerry were also present. Flanagan surprised Bosch while he as handcuffing Tom and Jerry. Bosch's partner, Jerry Edgar, then surprised Flanagan, allowing the two cops and Wish to escape.