Granger wasn’t working with the needle guy on the boat. He had been feeding hand-picked information to his army (marine?) buddy, who was feeding it to the needle guy, who was working for the Chinese. This had been going on since he was in the academy for the FBI.
I forget which Agency Granger was working for (he had reported being approached to the proper authorities), but he was in jail, then broke out of jail with his buddy. They were supposed to run up the line, so that the Agency could get the bigger fish, but the first fish up the line was needle guy, and he was a distrustful sort who wanted information and didn’t mind leaving a corpse. The Agency lost track of them and things were looking dark for our hero.
If the FBI and the magic numbers hadn’t found him in the nick of time . . .
Don’t remember the other two guys or how they fit into the arc. Unless the Afghanistan guy was the scientist who was locked up because he had sent his crop research to Afghani scientists. Someone in the government had reviewed his work and said it could be used to genetically design human pathogens. If that’s the guy, then Charlie sent the rest of his research to the same Afghani scientists, to help fight famine. Charlie lost his clearance and had to work for LAPD instead of the FBI for a few episodes, until he got cleared and got the clearance back.