So about a half hour ago i had just finished killing the final boss in the DLC, getting the treature and making my way back to Shades. upon turning in my mission i notice that what i had just finished doing (going to kill the final boss) is there again. the mission briefing says for me to do the mission again, but upon going to the location, nothing was there. I went back to Captain Scarlett to see if she had anything for me to use and nothing. so i'm pretty confused as to what it really wants. She has nothing and couldn't find anything at the top of the tower.
anybody have a clue?
You have to do the mission as you originally did, AKA: start in Wurmwater and open the lever that opens the gate into Magnys Lighthouse, then it should progress as normally.