Kinda hard to see.

At the bottom is the tunnel entrance. Next to it is the Apprentice's Den. To the right, we have the Nursery, and in the very center is the Meeting Rock, along with the Leader's Den. Next to the rock is the Warrior's Den. To the felt is the Medicine Cat tree. And there are at least two ventilation holes in the cave ceiling. There are also secret areas where cats have access to water underground.

Also, it's strange. How did a dead tree end up in a giant cave?

Water, of course! The New Lake (where LakeClan lives) floods washed the tree away, and deposited it into a newly formed cave.