As the name implies, the room is a docking bay for Escape Ships, with three ships visible in the bay in-game. However, the actual ships cannot be immediately accessed, as they are barred by gates marked with an emblem similar to those on Space Pirate vessels. The room is primarily composed of the purple mechanical structure present throughout the Mother Ship. Narrow shafts exist above and below the ship bay.
Samus first comes through the bay via crawling through the shaft beneath the room. Although she is attempting to stealth her way through the Mother Ship in search of escape, she is unable to enter the bay until she recovers her Power Suit, since the room is locked behind Red Hatches.
Following her recovery of the Fully Powered Suit and defeat of Mecha Ridley, the Ship's countdown sequence is triggered. Samus returns to the escape-ship bay, but is confronted by two gray Space Pirates.
After destroying them, the gates open and Samus is able to access the Escape Ships. A red Zebesian jumps out of one Escape Ship to attack her, but Samus is able to steal the ship for herself, flying out of the Mother Ship before it explodes. During the escape, a red Zebesian tries to climb onto Samus's shuttle, but is killed by the impact. The escape-ship bay is destroyed when the Mother Ship self-destructs.
The escape-ship bay plays a nearly identical role to the docking bay from Metroid: Zebes Invasion Order, another adaptation of the original Metroid that likewise adds a lengthy epilogue after Mother Brain's defeat.
Just like the escape-ship bay, the docking bay is a room inside a massive Pirate Ship that Samus boards after Mother Brain's defeat, and she comes to the bay to take a small spacecraft and escape shortly before the large Pirate Ship explodes. In the Bad Ending, Samus goes to the docking bay without first retrieving the Metroid capsule, and she is forced to fight the dangerous Metroid=Mutant before escaping, similar to the difficult gray Space Pirates from Zero Mission. The Pirate Boss may also appear in the docking bay, killing Samus with a large caliber beam cannon. Otherwise, if Samus retrieves the capsule from the command room first, she is able to escape the docking bay without any further interference.
It is unknown if Zebes Invasion Order had any influence on later Metroid games such as Zero Mission. It is possible that the escape-ship bay was directly inspired by the docking bay from this book, or any similarities are merely coincidence.
- This room's battle with the gray Zebesians becomes extremely difficult on Low Percent Runs of the game, as Samus can easily be killed if she has not obtained enough Energy Tanks. One tactic is to kneel by the ledge and shoot the Pirates as they ascend the wall, allowing Samus to kill them without taking any damage.
- It is not necessary to kill the red Zebesian that jumps out of the Escape Ship. If Samus chooses to spare it, there is a chance that the second red Zebesian that enters the room may end up carelessly shooting and killing the first Zebesian during the following cutscene.