Scene 2: The BridgeThe boats then goes past a illuminated screen with the silhouette of the captain, drinking from his mug. The 3 penguins then emerge and whack the captain unconscious, before taking control of the steering wheel.
Scene 3: The StormThe boat the goes into another room. A(n animated) porthole offers the guests a view of the choppy seas outside, along with a crate floating on the sea. The room is dimly lit, and to heighten the tension and make the experience more authentic, wind is blown onto the guests and sirens blare.
The boat then floats past two tall stacks of crates. One of the crate stacks suddenly collapses, almost threatening to hit the guests. Effect is achieved by sliding individual crates away from each other. See diagram.
Scene 4: The Beach-up Scene 4: The Beach-upAfter the storm, the boats beached up in the calm sunny beaches of Madagascar. Alex is the first character to be seen, breaking out of his crate. One interesting detail is the "days without steak" carving on his crate. Then it is Melman, with his signature complains about his sickness. Gloria then appears, with starfishes covering her essentials. Finally, Marty appears, lounging in his party hut, apparently getting very comfortable in the new environment. One fun thing to do is to look back, and you will see the other side of the cargo ship, as well as a huge anchor in the sand.
"Alright boys, party's over" - Gloria
"This is frak-a-lacking" - Marty
Scene 5: PenguinsIn this scene, the 3 penguins are studying the map of Madagascar.
"This map's written in code"
"We are going into hostile territory"
- Skipper
Scene 6: Danger AheadThis section takes place in a heavily themed jungle section, with low ambient lighting and fog effects. We start with seeing Melman looking at the "Turn Back!(Before it is too late)" sign. Then Marty appears, with half his butt being swallowed by a carnivorous plant. A fun thing to look out for is a hidden "Kuala Lumpur 354km" sign. Then there are more carnivorous plants along the trough, and the soundtrack here is foreboding.
The next section starts with Alex stuck on a spider web, and Marty trying to help him out. We move on to see more spider webs, with spider animations squeaking "How'do you do?" in incrementally higher pitches. We also go past an animatronics crocodile, and see Gloria swing overhead on a snake.
This is also where the entrance to the maintenance dock for the boats are.
In the next scene, we see the monkeys, and they start flinging poo at you, rather unexpectedly. (The poo is actually water)
"If you have poo, fling it!" - Monkey
Scene 7: Move it Move itAt the entrance to this scene is a pair of giant green leaf-like gates, with projections of the silhouette of small animals dancing. The door then opens up to reveal a party in full swing. The lemurs are dancing to the beat.
Scene 8: FoosaKing Julien informs the "New York Giants" about the foosa attacks, and the gang are determined to fight the foosas. As the boat turns a corner, we see the Mort (the small hamster like creature that got chased by a shark in Madagascar 2) being seasoned by the foosas.
Scene 9: The planIn this scene, we see King Julien planning the foosa attack in front of a giant model and map of Madagascar island.

"I came up with it! Me! Me!" - King Julien
Scene 10: PreparationWe see King Julien introducing his "Wonderfully camouflaged fighters". Marty is dressed as a trojan horse, Gloria is trying desperately to fit into her overly small outfit.

As the boat take a turn, we see the penguins having their own plan. They are preparing explosives to chase away the foosas.
Scene 11: The showdown
We enter the foosa's volcano through a foosa shaped cave entryway. This is a wonderfully crafted area, with smoke coming out of the mouth, fire in the eyes, and lots of foosa shadows running around the entryway.
This entryway leads into the main room where the gang are fighting the foosas. This takes place in a volcano caldera. Fountains of water are lighted red to mimic boiling lava. Alex is owning the foosas, swing one by the tail, Melman is knocking the Foosas out with his head, and so on.
As we turn the corner, we see the penguins throwing King Julien a bomb. The bomb explodes, and destroys the foosas, leaving a rather smoked King Julien.
At this point, the boat inches nearer to a waterfall that spans the entire boat channel. Just was the "bomb" explodes, the waterfall stops and the boat passes under it.

Scene 12: Celebration
In this scene, we see the animals celebrating their victory over the Foosas. We see a giant "Thank you freaks" banner over the boat channel, we see the animals dancing to the music. There are even bubbles being blown at the boat. We see Marty lounging on his chair, sipping drink out of a coconut, and spitting the drink on the guests.
We also see the plane trying to take flight(a scene from Madagascar 2), with smoke coming out of their propellers. The ride ends here, and the boats come out of the show building, back to the loading/ unloading dock.
The guests are then directed into a gift shop where they can purchase their on-ride photos.