The Bunker was originally built as a place to store the damaged Potatoes after it shut down near the base. W4stedspace needed to repair it to get the coordinates to Dr Morphologis's location. Haunted by strange dreams, W4sted's paranoia went to a whole new level, resulting in significant security enhancements to the base, including 2 small turrets and fortified hangar doors.
Several projects in the series were born in the base, including Ed, a bipedal mech, the Mag-Bike, the Workbee, and General B ATV. These projects required additions to the bunker, such as a vertical-launch tube for Ed, storage room, control room, sleeping area (not that he slept much) and an area where he kept digging out for no reason.
w4sted's w4sted bunker, as seen in Episode 9, "The War Within"
In the drone retaliation between Season 1 and 2, w4sted's bunker was largely destroyed. The initial attack, an artillery strike, happened when he was in the main bay itself. Subsequent attacks completely wrecked the main bay, but many of the caverns and some of the projects underneath remained intact.
In Season 2, Episode 9, "The War Within", w4sted reveals to the other Survivors that something strange existed at his base - a vertical shaft with an unknown terminus. He had subconsciously drilled a path to this shaft, initially thinking he had been dreaming that act but realizing he had been doing it while awake. Considering that his dreams also include falling down this shaft, it is not sure if he has actually been down there or not.