Deep Cover is a story about a submarine sailor, Bailey Jones, who is assigned to a government school for special training. This school trains him to become a secret agent. When Bailey finishes his agent training, he is assigned to a number of government covert missions, which are classified TOP SECRET, each mission is a little more dangerous. Because Bailey and his partner, Jan, have performed so well as a team, they are transferred to the CIA. Bailey and Jan fall in love and they get married While they are on assignment in Pakistan, Jan is killed. Bailey handles his sorrow by continuing to stay in Pakistan and carry on his assigned missions, however he becomes a favorite target of the terrorists and international illegal drug organizations that dominate the middle east. Bailey relaxes his vigilance and is ambushed by killers working for the illegal drug lords and is nearly killed. When Bailey has recovered, he returns to duty in the middle east working alone. Because the Agency identifies a security leak, he is assigned deep cover status by his bosses at the CIA. Bailey eventually requests a female partner, Sarande. After Sarande makes some personal adjustments, they participate in the initial planning for the invasion of Afghanistan.