4 Hours might have done what you needed to do, but all you do now is Open a Hatch Top Middle then enter, from the Sewer go back to the Laboratory. Linda is in the Deserted Military Base just make sure to Bring some Angel Milk, they can be pretty tanky down there, save often the enemies are composed of Bad End scenes when defeated!
PS : You are Naked the whole time so grind the Gym before you try!