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Smash Brothers Reference
Use the Silver Bow on chapter 8 for an entertaining conversation between Palutena and Pit.

Space Invaders Reference
Pit calls the aliens who invade Earth "Invaders of Space."

The Legend of Zelda Chime
When you solve a puzzle in the Wish Seed level, a chime similar to the Legend of Zelda plays.

The Legend of Zelda Fairy Reference
The description of the Fairy Orbitars idol starts with the sentence "Tired of pixies asking you to listen?", a reference to Navi in The Legend of Zelda: Ocarina of Time.

Vintage Kid Icarus Reference
When Pit sees the box holding the three weapons, he declares "They've held up well" and Palutena mentions how "They're much less pixelated now." in a reference to his first game. There are lots of images and references to previous Kid Icarus titles, such as when Medusa is first shown in Lv 1.

Metroid Reference
When you are playing the ground battle on Heads of the Hewdraw the Komayto appear as an enemy. Though they appear more through out the game. During the ground battle on The Chaos Vortex, during the eigth wave, Viridi and Pit have an arguement about the Kotmayto's simularity with Metroids.

Dr. Mario Reference
When watching the powers tutorial video, Pit mentions that playing Dr. Mario pays off when arranging powers on the power grid.

Game & Watch Reference
On the ground stage of The Chaos Vortex, during the third wave of enemies, Pit mentions how the jerking motions of the Aurum in this wave are simular to the Game & Watch.

Donkey Kong Reference
On the Ground stage of the Lightning Chariot, there is one room where you need to use jump pads to get over some rolling spheres. Pit says it looks familiar as Hades says "I guess the Chariot Master has played Donkey Kong."

Nintendogs Reference
In Chapter 9, when entering the Twinbellows chamber, Pit will directly make a reference as he mentions how he is going to rack up Nintendogs Trainer Points with Twinbellows.

Star Fox References
In Pandora's Labyrinth of Deceit there are several areas that resemble past Star Fox titles including Star Fox 1, Star Fox 2 (never released), the bonus asteroid zone from Star Fox 64, and Star Fox Assault.

Cave Story Reference
In the power tutorial video, Palutena tells Pit that he won't be fighting alone out there. And then Pit says "You're going to send me a machine gun robot girlfriend?". He was referencing Curly Brace from Cave Story.

Spinning Pit
On the 3ds menu before you start the game, blow into the mic and you will see pit on the top screen spinning.

After Credits Hades Threat
Wait around till roughly five minutes after the credits roll and Hades will threaten to delete your save file.

Moving Menu
If you touch the icons on the menu screen, you can move them around

Credits Mini-game
During the credits when you beat Chapter 25, you can shoot the words and names and they will turn red. Your score for the number of words and names you shot will appear after the credits. You can also move Pit, use charged shots, and aim your shots with the touchscreen

Brain Training Reference
On the level were you play as Dark Pit. Dark pit advises Hades to "break out the BrainAge," and then Virdi comments on her BrainAge being 24

THX Sound Effect Reference
As Pit is shown approaching the entrance of Dyntos' workshop near the end of the Chapter 24 Air Battle, the LucasFilm THX Sound Effect is heard.

Annoy the Fiends Cauldron
Repeatedly tap the face of the Fiends Cauldron and after about a minute it will turn around, infuriated by your persistent tapping. Ocasionally it will turn half around and glare

When you die, hold down when the FC drops your hearts. Don't let go. Enjoy.