Based on what we've known so far
- In the film, the filmmakers purposely made it the same time of year it was at the beginning of the first film, at the end of this film... that way the city was just like it was before they left.
- DuBois and her men are on their way to Madagascar, where Julien's subjects and the foosa are. It is unknown what'll happen to the lemurs of the kingdom.
- The island of Madagascar does not appear at all in this movie nor is it mentioned out loud, though this is the location that DuBois and her allies are being sent to at the end of the movie as seen on a box on the frieght ship.
- The official junior novelization of the movie mentions the Penguins using a giant mechanical penguin-bot to fight Dubois in the climactic final scene, which Skipper refers to as having been built in anticipation of Y2K but was never used in the end. This never actually takes place in the movie, presumably to Kowalski's chagrin.
- Kowalski's iconic abacus makes its second appearance in the films.
- During the movie, you could see animals from the previous movies and series.
- The way the plane crash lands is the same way it did in the second movie but in the second movie Gloria was asleep but this time she was awake.
- A reference to the first movie is made in the way DuBois and her men are stacked up in crates in the same way Alex, Marty, Melman and Gloria are stacked up in the first movie.
- Alex's birthday at the beginning of the movie is the same as Marty's in the first one. But, the wishes are different. In the first movie, Marty wishes he could go to the wild. But, in the third movie, Alex wishes he could go back to New York City's Central Park Zoo.
- This is the first time in the movies Julien saved the day (not counting the original movie when he and Maurice stopped Alex from going bezerk and nearly eating/hurting Marty.
- The ship from the first film reappears although it should still be on Madagascar. Then again, a possible reason for this is that it was found by a visitor to Madagascar, although this still does not entirely explain the reason.
- Marty's "Afro Circus" song has become a popular fad on YouTube, being used in remixes and edited videos.
- Zuba and Florrie were originally supposed to appear but they were cut. If they did appear Sherri Sheperd would reprise her role as Florrie and Samuel L. Jackson would've replaced Bernie Mac (due to his death) for Zuba.
- In the shot of New York's skyline shown in the scene the animals return to the zoo, the new World Trade Center towers are visible. However, the complex was not incomplete by the release of the film, and One World Trade Center should be seen under construction.
- In the international version, a Wilhelm Scream can be heard when a motorcycle rider crashes out of the freeway during the car chase scene.
- It is in Madagascar 3 that Rico's love of violent explosions is cemented; not only does he set up things like the cannon filled with TNT, and the rocket shoes for the dogs, but right after Stefano is first fired out of his cannon, Rico is seen cuddling a stick of TNT affectionately.
- At least three out of four of the penguins cheat at cards - Skipper, Kowalski and Private all have four Aces in their hand, but we don't see Rico's hand.
- This is the second time in the franchise where Gloria gets stuck due to her fat body and butt (going through the pipes in the opening). The first time was in the plane door in the beginning of the second film.
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