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Jakobs Cove, like other locations in Borderlands, has several sub-sections and a main hub, as follows:
Jakobs Cove: The actual town of Jakobs Cove acts as the area's main hub (housing the bounty board and vending machines) and allows access to all of the other areas.
Hallow's End: A swamp populated with hordes of undead which rise from its shallow waters. This section of the map is also home to Dr. Ned, who lives high up in a tree-house-like hospital/clinic which safely houses the seemingly well-meaning doctor from the undead. The house is only accessible via an old freight-style elevator which Ned must hand crank from above. T.K. Baja also owns land in this portion of the map, and there's even a pumpkin patch.
Generally Hospital: A creepy, horror-influenced hospital that sits alone atop a hill with a cemetery at its base. A beach area surrounds most of the hospital.
Dead Haven: The same city visited by the player in the main Borderlands storyline, but with an undead makeover. The city is now a ramshackle ghost-town/Hooverville populated by legions of shambling zombies and undead Lance. The player is tasked (albeit unwillingly) with addressing the "living-impaired" problem caused by the Jakobs corporation. This town is also home to a recently unemployed "associate" of Dr.Ned to whom the player must deliver severance pay.
The Lumberyard: An expansive mill and yard area. This is also the last section of the map associated with the main quest in the Zombie Island DLC.
The Lumbermill: Dr. Ned's last refuge, where he and the player have their final showdown.