- "A small submarine... A submarine?! What on Earth was a submarine doing there?!"
- — Junpei, looking around while comforting June
The Storage is a room located on the C Deck of the Gigantic/Building Q. It is a large, open room with a small staircase and a submarine placed inside of it. It is found behind the Sun door and is only accessed during the Submarine Ending.
The Storage is a huge room with metallic walls. There is a staircase leading from the automatic doors at the entrance and a yellow submarine in the corner of the room, in a pool of water. Lighting is located on the ceiling.
After Junpei, Seven, and Lotus escape from the torture room and see the bodies of Ace, Santa, and Clover strewn along the central staircase, Seven finds that Clover does not have a pulse. However, he does not check the others, due to Lotus's warning that the murderer might come back. She takes the Sun key and the group runs to the Sun Door to unlock it. Surprisingly, the door has already been unlocked. They rush through it, running down the hallway. Finally, they come to a set of double doors.
While pondering how to open the doors and thinking about going back, they find that the doors open automatically. While Seven and Lotus are shocked about this, Junpei rushes in and to his utter shock, sees a dying June on the floor of the room. He goes up to her and has a heartfelt, touching moment with her. She admits that she's liked Junpei for a long time, and that she will never forget the memories of the time that they spent together in elementary school. June dies in his arms and he cries until he has no tears left. The clock bell rings 5 times, and Junpei realizes that he only has an hour left before the time limit is up.
Suddenly, he notices that Seven and Lotus had not followed him into the room. He goes back through the double doors and finds them gruesomely murdered, with Lotus's bracelet gone. Realizing that he is the only participant alive, he stumbles over to the submarine in the room. As he is about to get in, he is stabbed in the back by Ace, who had faked his death. Junpei falls into the water and dies, unable to see who his murderer was. Right before dying, he wonders who had killed them all and has flashbacks of all the murders that have occurred.
- Because the Sun Door was already unlocked, the Sun Key is never used by Junpei.
- The room's name is shown on the C Deck map for an unknown reason, being that it is not an escape room and it is only traveled to in one ending.
- The Submarine Ending occurs here and is the only route where Junpei or any of the other characters will ever see this room. The answers to whether or not the submarine could be opened nor what was inside were never revealed.
- According to why the submarine is there: "In the events of nine years ago, one of the researchers hired by Gentarou Hongou had a crisis of conscience and prepared the submarine to rescue the kidnapped children. A replica of the submarine was also installed at Building Q."
- The submarine may explain how Hongou was able to survive the sinking Gigantic.
- The only reason why the submarine is in Building Q is so that it would be an exact replica of the Gigantic. It is unknown if this submarine is functional. However, Q49 of the Answers reveals that the submarine wouldn't lead anywhere and would just hit a dead end.
- The direct translation of the Storage's Japanese name is "Hangar".
- In Zero Escape: The Nonary Games, the trophy/achievement "We All Die By a Yellow Submarine" is earned upon receiving the Submarine Ending. This is a parody of the Beatles song "Yellow Submarine" which contains the lyrics "We All Live By a Yellow Submarine".