Before SEMME, Anthony McHenry was the son of a scientist who worked in Area 51. After Mr. McHenry stole a Martian Saucer, Anthony McHenry Sr made a bargain with the US Government: in exchange for his father's life, he would work for them as a secret agent. He and Linda Walkerton became the first "official" SEMME agents before there was such a thing. After Linda's 'retirement', he became the head of the organization that would eventually become SEMME.
Big Boss was captured by the Head Alien during an assault on the SEMME headquarters and placed in Monkey Master's (somewhat ineffective) 'Tummy Prison'. He was quickly rescued by Squadron 128, shortly before detonating a bomb on Monkey Master.
He was later killed at a mission at the Martian Embassy, fatally crushed by falling tubes containing the bodies of Sal Walkerton's adoptive parents. These crashed through the ceiling after being dropped on the Head Alien by Walky in the room above. The agents on the scene attempted to resurrect Big Boss using the advanced technology at the Martian Embassy. They were prevented in doing so, however, when Monkey Master destroyed the entrance to the Martian Embassy in his own effort to revive the Head Alien.