The Holes are a shortcut from Hideout 4 to the area near the Radio Tower. It is highly recommended to discover those first, as you need a lot of time to investigate the Radio Tower and find your way to the Radio Bunker Underground entrance.
There is a crate and something in the smaller holes who tells you to leave:"these are my holes".
In the crate are planks, fuel, a lantern and pincers!
- spoilers. Reader discretion is advised.
If you didn't kill the Doctor in chapter 1, you can find him near the cart outside the holes. He is sitting and smoking - looks like in a late state of an infection. You can talk to him and get some Gospel options, to find out more about his story.