Rayquaza is the second boss in adventure mode of Super Smash Bros. Brawl. In the Subspace Emissary, Rayquaza first appears in the jungle after Diddy Kong goes to investigate a crashed Arwing. It bursts out of the water and destroys the Arwing with a Dragon Pulse attack, then grabs Diddy. Before it can try to eat the helpless monkey, Fox McCloud leaps from the burning Arwing and attacks Rayquaza using Fox Illusion, causing it to lose its grip on Diddy Kong. The beast attacks Fox with the lightning orb again, but Fox reflects the attack back at Rayquaza using his Reflector, sending it tumbling back into the water. Both Diddy and Fox face off against the dangerous Legendary Pokémon. It can also be battled at any given time in the Boss Battles mode.
It has not been proven to have any connection with the Subspace Army and could just be angry at Diddy and Fox for intruding on its territory (seeing as legendary Pokemon are extremely territorial) however what is so unusual about this is that lake being Rayquaza's territory and in the Pokemon anime/story Rayquaza's natural habitat is the ozone layer and has not been known to be able to swim as it was shown when Rayquaza appears out of the lake. However, in the last level, Tabuu resurrects Rayquaza to slow down the heroes in the maze it creates out of previous worlds. Also, when Rayquaza is defeated, it twitches at the last second, which probably means it was only knocked out (a possible throwback to the Pokemon series, where a Pokemon who is defeated in battle is said to have fainted). Rayquaza is level 5 in intense mode.
Dragon Pulse: Rayquaza sends a ball of electricity in front of itself diagonally, or lowers its head and sends the lightning orb in front of itself, which travels across the stage unless it hits the ground, when it will explode (This can be reflected by various reflecting attacks but not absorbed by PSI Magnet or Oil Panic).
Dig: Rayquaza burrows underground, then bursts out of the ground where the player was standing. At lower HP, Rayquaza does this three times. When its HP is low enough that it can be captured, it will perform this attack four times. A suicidal move if used against Marth and Ike since they can easily Counter it to massive damage without taking any damage.
Earth Power: Rayquaza's eyes glow, and then it creates an explosion at the location where the player was at that time. While Rayquaza's eyes glow, fighters in contact with its head will be spiked to the ground, often a perfect setup for the explosion.
Thunder: Rayquaza flies up in a tight circle and hits you with a multi-hit lightning bolt (it does not have knockback, however). It breaks shields down quickly. During the time Rayquaza rises touching it will deal Electric damage. It's one of the few attacks that are easier to dodge on higher difficulties due to its much shorter duration. Rayquaza only uses at lower HP.
Fly: Rayquaza flies up slowly, then crashes into the character while burrowing into the ground, then appears on the other side. The above lightning bolt attack is the substitute for this at lower HP.
ExtremeSpeed: Rayquaza flies up, and then dashes back and forth near the ground. At lower HP, Rayquaza does this two or three times. Small characters can evade this attack by ducking if they can fit between the "waves" of Rayquaza's wavy shape and the ground, but the move also produces a wind that can push characters around (making crawling an asset) into a spot where they can be hit.
A Sky High Pokémon. It normally resides high up in the ozone layer where it flies endlessly, so it is rarely seen. However, when Groudon and Kyogre began to fight, it appeared to calm them down. It has the ability Air Lock, which blocks all weather-condition effects. It has exceedingly strong abilities, and its attack power is especially remarkable.
Rayquaza has a lot of Health which can make fighting it rather difficult to destroy effectively. It also may resist many different kinds of attacks. Strangely enough it is not particularly weak to Freezing attacks (in the Pokémon RPGs, Rayquaza is especially vulnerable to Ice). Ganondorf's Darkness attacks are not resisted by it, in fact Rayquaza may be weak against them (which also, coincidentally, doesn't make sense in the RPGs).
Despite being the "Sky High" Pokémon who lives high in the ozone layer, Rayquaza in Brawl seems to be able to live underwater (although in the game, it is capable of learning the move Dive; or might possibly be sleeping there) and attacks by burrowing underground (it cannot learn Dig in the game). The Pokédex says that Rayquaza never touches the ground, however, unless Groudon and Kyogre were to fight.
A glitch can happen when facing Rayquaza. It is unknown how this happens, but it can leave some of your character's model stuck frozen in the immediate foreground, moving with the camera. Any attack Rayquaza performs that targets the player's location go offscreen, failing to hit the almost-KO'ed player. This glitch lasts until you quit the battle. Here's a video showing the effects of the glitch.
Rayquaza is the only boss fought at the beginning of a stage. Galleom and Duon do not count, as they essentially are the stage.
Rayquaza is the only boss in The Subspace Emissary known to have a specific voice actor (Katsuyuki Konishi).
Rayquaza is the only boss in The Subspace Emissary to be from the Pokémon universe.
Rayquaza may be a boss in The Subspace Emissary, but that does not necessarily mean he is a part of the Subspace Army. He might have just been disturbed due to the crash-landing. This is also possible due to legendary Pokemon being very territorial.
The Rayquaza in the Great Maze might be a copy of the real one.