The best way to do it, in my opinion, would be to reveal a larger conspiracy backing stryker in his mutant experimentation. they send a team to 3 mile island and recover "Weapon XI"'s body, only to discover that he survived the decapitation and his healing factor has burned itself out from the strain. they take the unconscious Wade Wilson/Weapon XI to "The Hospice", a place for failed experiments run by Dr. Killebrew. we learn that Wade's body is slowly rejecting his implanted mutations, and killebrew surgically removes the retractable blades without the use of anaesthetic. wade escapes his restraints and lashes out at the doctor, nearly killing him. he is punished by execution, an act which both re-activates his healing factor, and acts as the final straw in his complete mental breakdown. the re-activated healing factor has mutated within wades body, and purges him completely of the remaining implants, but since the healing factor is constantly attacking itself as a foreign strain in wade's system, his skin becomes a constantly shifting cover of scar tissue. returning from near death for the second time, wade destroys the hospice, frees the other prisoners, and finally adopts the name Deadpool (both because of dying twice and hence beating the odds in a hypothetical deadpool, and a somewhat sardonic acknowledgement of stryker's christening of him). he also salvages the adamantium arm blades and turns them into customized katannas. the rest of the movie could play out as a twisted revenge film, with deadpool setting out after the organization behind stryker's experiments in his own derranged way, and end the movie as the merc with the mouth that we all know and love.
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