Scrambling through the dense jungle in search of help, Diddy Kong stumbles across a lake where the wreck of the Arwing can be found. Either the crash or Diddy's presence must have disturbed a powerful beast that resides within the lake. Rayquaza, the legendary Pokémon and master of the weather trio. It launches a powerful shot at the Arwing, setting it into flames, then grabs Diddy Kong while it soars into the air. At the last moment, Fox jumps right out of the Arwing's burning fuselage, frees Diddy from Rayquaza's grasp, and deflects an attack back to Rayquaza. As Rayquaza is reeling from its own attack, Fox invites Diddy Kong to join forces with him and take down this fearsome monster.
Boss Battle: Rayquaza
As the second boss you face, Rayquaza has a more diverse moveset than Petey Pirahna. Despite its low health, it is resistant to almost any type of attack you can throw at it, especially projectiles, so you must get up close if you want to deal any significant damage. Fortunately, Rayquaza follows an attack pattern that can let you predict its next attack and prepare to dodge it.
Rayquaza's first attack will either be swiping at you with Iron Tail or rush to the opposite side of the stage. You can dodge both by jumping high and airdodging as an added precaution, so it isn't a big threat. Its next attack will be to launch an energy ball diagonally toward or parallel to the ground, or use Dig to enter the ground and burst through from below. The energy ball is slow enough to be easily dodged or reflected, but since Rayquaza has a strong resistance to projectiles, it's not really worthwhile. You can dodge Dig by running around the stage while its underground, causing it to miss your location when it emerges. Note that Rayquaza will start bursting from below three or four times as its nearing death.
The move after that is the trickiest, as there is a lot of moves that Rayquaza can use against you in this stage of the fight. It can swoop across the stage, which can be dodged by a well-timed air dodge or by simply ducking, though it will start doing it a few more times when its health is low. It can also cause explosions where you're standing by sparkling its eyes, which requires you to quickly move out of the way as soon as you see the spark to avoid the attack. It can also fly up and shoots into the ground, then simply appear at the opposite end of the stage. Finally, it can form a circle with its body, striking the ground with a lightning bolt. Simple dodges are enough to evade these two attacks.
Having defeated Rayquaza, Fox decides to part ways with Diddy, but the monkey insists otherwise. He drags Fox along with him, trying to get Fox to help him save Donkey Kong.
The forest by the lake
The mechanics of this level can be confusing. There are two versions of this level with different obstacles and pathways, and you must travel between these two alternate versions using the doors marked with arrows to make it to the end. Start of by entering the yellow door, which will take you to the alternate level, bypassing the wall that was here before.
Move right and destroy the wall of blocks, then enter the blue door under the ramp to return to the first version of the level. Move left, returning to the opposite side of the wall to find a gold item box. You'll encounter some Auroros in this level. These swan-like enemies jab their beaks straight into the ground, after which you can pick them up and throw them like an item.
Continue right and fall down the giant hole to progress. You'll face some Red Paratroopas while falling down the shaft, so either evade them or dispatch them as you reach the ground. Go through the door at the bottom.
As you enter the room, there will be a split-second flash that indicates that you are surrounded by multiple blocks. The room will then be cloaked with darkness, so jump up an attack the bomb block at the top-left of the wall of blocks to destroy all of the blocks surrounding you, lighting up the room at the same time. You can find a blue item box at the top-left, but you must go right to advance.
Jump up the various platforms and climb up the ladder flanked by many Hammer Bros. At the top, move to the left and enter the blue door there to return to the alternate section of the level. Move right and defeat the Towtows and Auroros to reach the red door, which will take you to the next section.
The tunnel in the cliff
Moving to the right, you will encounter some Bucculus. These vicious creatures stick their red lips above ground, then jump up and sticks to you when you get close. It attacks by draining your vitality, filling up its poison sac, but defeating one with a full poison sac will likely net you a Maxim Tomato. There are two doors here, one red and one yellow, but you want to ignore it and go down the Bucculus-filled tunnel. At the end, you can find a blue item box with a nice extra life.
Move back and enter the yellow door, then move down the same tunnel in this parallel level to enter a fight against some Goombas. Once you defeat them, attack the bomb block to cause an unseen change in the other version of the level. If you return to the parallel version of the level through the blue door, you will find that a section of the ceiling in the tunnel has opened up, revealing a switch.
Now, enter the red door. Having hit the switch, you've now disabled the flames that would've prevented you from progressing if you entered this room earlier. The door that leads to the next section lies in the dimension with the yellow doors, guarded by a Towtow, but you can access it from the parallel dimension by entering the blue door in the corresponding room.
Rapid raft ride
Through the door, you will end up on a raft on a raging river. Enemies will frequently assault you, so take care of them as fast as you can to avoid being overwhelmed. You will come across a blue item box, a floating platform with some Hammer Bros that you can defeat with the force ball on it, and a midair door. Enter this door to reach a secret room.
In this room, there are two force balls, one blue and one gold item box, and a lot of unbreakable blocks. Use the force balls to break them all, then collect the items in both item boxes, which contains a trophy and an extra life. Return to the level through the door you came in. Past the midair door, Bullet Bills will start flying at you, followed by the appearance of a gold item box. Break it open to obtain its contents, then fight some more enemies until the raft reaches shore.
Move to the right, defeating the numerous Goombas, Koopas and Hammer Bros. Keep moving until you reach a cannon, which will launch you in a weird, spinning flight path across the sky and into a pit.
You'll be forced into a battle with a Bowser created by Shadow Bugs. This version of Bowser is no different than the normal Bowser, being slow but hard to KO. If you managed to retain your stocks across the level, you'll have a natural advantage against him.
Having reverted Bowser back into trophy form, Fox and Diddy only have a short time to celebrate before the trophy dissolves into Shadow Bugs. Two Dark Cannon shots flies toward the pair, which both narrowly dodge. It turns out that Bowser has led them into another trap, using fake Bowser to lure them into the area. While Diddy Kong wants to avenge his lifelong friend, Fox sees no benefit in fighting. He grabs Diddy and runs off the cliff.
Once you beat this stage, Fox will join your team!