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The storyline picks up a while after Instincts. Jack is hired by a woman named Kade for an arms deal between pirates and the government in Micronesia. The deal then is under attack by rebels led by a native Chieftain named Semeru, who along with his elite warriors, exhibit the same feral abilities as Jack, who is framed for the attack.

After fleeing to a safehouse with Kade, Jack is confronted by Doyle, who is here for damage-control. He offers Jack and Kade amnesty in exchange for their help in destroying a refinery under rebel control. After successfully doing so, Doyle is wounded and Kade is captured by rebels. Jack saves Doyle due in part to him knowing the way out of the jungle, but while finding transport, Doyle is captured by rebels. After tracking Doyle's blood through the jungle and a base built in the forest canopy, Jack finds Doyle dead at the footsteps of a mountain temple.

Jack then makes his way through the temple where he encounters Semeru again, who taunts that without focus or devotion, Carver is just a fake with powers he does not deserve. He then captures Jack and reveals that Kade gave him the money from the deal, as well as to help kill Jack. Kade then wounds Jack before Semeru attacks him. Jack manages to defeat Semeru, and kills him by impaling him on bamboo rubble. Carver then confronts Kade, who pleads that there was no other way she could save her own life. Instead of killing her however, Jack gives her back the deal money saying "Save your tears. In another time I would have done the same. It is all too... human".