[Season 1]
The first season revolves around the cases handled by a special division of the Naval Criminal Investigation Services based in Los Angeles that deals mostly on undercover work and counter-terrorism. The focus is on team leader G, Callen, a silent, collected undercover expert who does not know his past. He and his team face off zealot terrorists, drug lords and other baddies with high tech surveillance and high octane action, while their agency's director fends off political undercurrents and bureaucratic red tape.
Because of counter-terrorism plot lines, Season 1 also touches on the religious beliefs of jihadist terrorists and extremist groups.
In the episode 'Brimstone', the suspect of a few killings is a Muslim ex-Marine, but it turns out to be a disturbed, overzealous Christian.
In another episode 'Chinatown', the themes of suicide and homosexuality are explored as a gay naval officer is depicted taking his own life by jumping off a bridge with a noose around his neck.
[Season 2]
The second season revolves around cases handled by a special division of the Naval Criminal Investigation Services based in Los Angeles that deals mostly on undercover work and counter-terrorism. The season also reveals that Agent Callen may not be alone as he thinks as he may still have a family member left who he does not know of..
Season 2 also has some episodes that deal with counter-terrorism, and involve terrorists and extremist groups.