The books main conflict is centered around Richard's assignment as the leader of a new unit in the Navy, which he personally designs, SEAL Team Six, a counter terrorist unit. At the same time, Richard makes many enemies in the armed services. This is intensified by his formation of the so-called Red Cell, a special forces unit to test security at U.S. facilities. Richard is targeted by a Navy judicial conspiracy and is forced out of the Navy and put in jail.
Rogue Warrior