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With Dr. Rot back in the picture, Wolverine must discover the secret behind Rot's twisted family and how they are connected. Meanwhile, FBI Agent Wells circles closer to the truth behind the brutal murders he's investigating.
Logan is held captive by Dr. Rottwell, and the evil doctor goes about telling Logan about his family and his plan to unleash a new God Brain Machine. One bigger and more powerful then the last one. Dr. Rot also goes on to explain that the Flesh Puppets he had made are all from pieces of Logan's brain that he took years ago.
Dr. Rot torques Logan until he passes out. When Logan awakes he is a basement with a bunch of corpse. He escapes and kills Dr. Rot and his family but when he finds Baylee she has Melita. Logan berserk and after ripping Baylee up he kisses her.
This is when it is revealed that Logan's escape from the basement was just in his head and Tater is now in charge of Logan's body. Also it is revealed that Melita and the FBI are approaching the Rottwell estate with no clue what they are in for.