He may have killed Morgan while he was good. Remember, she is the most feared pirate hunter in the Caribbean. Maybe when LeChuck landed on Flotsam, he decided to steal some jus de vie before submitting to Flotsam justice, in case Grindstump would immediatly sentence him to be executed or Guybrush wouldn't be able to cure the pox and free him fast enough. So he sneaks into DeSinge's laboratory, and there is Morgan LeFlay. As far as he knows, she is a dangerous pirate hunter who is working for De Singe and apparently protecting his laboratory, and he knows he can't defeat her now that he is human, so he sneaks up on her and runs her through with her own sword. After that, maybe he finds some jus de vie, maybe he doesn't, but he submits to Flotsam justice anyway.
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