After successfully assissinating a "tinpot dictator" named Guerrera the biorg program is to be decommissioned. The military biorg program has successfully enhanced animals with custom hardware creating "Animal Weapon 3 (WE3)" which includes a rabbit (designed to deliver mines and poison gas), a dog (a small tank) and a cat (a lethal stealth machine). However with the help of Roseanne Berry the primary researcher the animals are freed.
After escaping, the WE3 are pursued by the military and ultimately defeat the soliders sent to recapture them. They are then attacked by biorg rats whom they defeat. Eventually the WE3 encounter a family out hunting who end up shooting 3 (rabbit) leading to 2 (cat) killing the family's dog and 1 (dog) killing the father. The son is later found alive. The military then plots their next move with "Animal Weapon 4"
WE3 are found hiding by a homeless man which leads the miltary to unleash WE4 (an enhanced pitbull) on the WE3. After battling WE4, 1 (dog) escapes and encounters Roseanne Berry who is then killed. This leads to a final battle with WE4 where he is terminated by the military. 1 (dog) and 2 (cat) escape, shed their armor and are rescued by Dr. Trendle who leaves them in the care of the homeless man who initially found them.