The level begins as Snake reveals himself from his cardboard box on board the Halberd (The box had previously been shown inside the ship). As he does so, he says his now-famous line, "Kept ya waiting, huh?"
After a section of the level, a hallway is shown, and Lucario and Meta Knight are seen rushing down it after they boarded the ship following the Glacial Peak. They go shooting past the cardboard box in the hall, but Lucario turns around and looks at the box with its Aura, and sees Snake's blue (good) Aura through the box. When Lucario lifts off the box, an exclamation point appears over Snake's head and the familiar "discovered" sound from the Metal Gear series is heard. Snake readies himself in an attack position, as does Meta Knight. Lucario, however, shows Meta Knight that Snake's Aura is good, so he is not an enemy.
Lucario then turns to look over Meta Knight's shoulder, again looking with Aura, and sees a group of incoming Primid and their intense red (evil) Aura, so the three advance to attack them.
Near the end of the level, the group comes to face Shadowbug versions of Peach and Zelda that were created from their caged trophies. After defeating the false versions, Peach and Zelda are freed from their cages and revived. Snake, however, motions for them to stay where they are. He leaves with Lucario and Meta Knight as the princesses exchange a knowing glance.
- Initially, Theme of Tara plays.
- During the cutscence where Snake meets Lucario and Meta Knight, Cavern plays briefly.
- After the three characters team up, Encounter plays.
- During the False Princess'sbattle, Castle/Boss Fortress (Super Mario World/Super Mario Bros. 3) plays.
When Snake reveals himself, he breaks the fourth wall asking the player "Kept you waiting, huh?".