The hall has two levels. The first one is partially underwater. The second, upper level is blocked by a barrier controlled by a Spinner that is located on the bottom level. Samus first enters it from a door out of the crashed Frigate Orpheon. As the name implies, there is a tree in the center of the room which helps Samus reach a higher ledge that can allow her to open up an entrance to the Life Grove.
- Hydro Access Tunnel (via Blue Door)
- Transport Tunnel D (via White Door)
- Great Tree Chamber (via Blue Door)
- Life Grove Tunnel (via White Door)
- Transport Tunnel E (via White Door)
- Lock (elevator side)
- "Gate lock engaged. The controls are on the other side."
- Lock (outside)
- "Gate lock engaged. The control system lies nearby."
- A Sequence Break can be performed here. By entering the room via Transport Tunnel D, and performing the Bomb-Trick to pass over the bars, Samus can enter the Phazon Mines without having to explore the crashed Frigate Orpheon or acquire the Gravity Suit.
- If this room is entered from Hydro Access Tunnel, the Crashed Ship theme keeps playing before Samus leaves the water at the bottom of the Great Tree Hall. If she enters the water again from the Great Tree Hall, Tallon Overworld will continue to play until she reaches the Hydro Access Tunnel.
- The White Door leading to Transport Tunnel E can be opened with the Phazon Beam (via hacking) and only from this side.