This didn't take as long as I thought it might.
Since Kohta referenced Brawl, I did too (hence, why I chose the Pokemon I did). I also played off the competitive nature between Fox and Falco that Kohta hinted at.
I didn't know what I was doing with the Pokemon, and I really wasn't going anywhere with it, so sorry.
But I'm sure Smashchu will have a ton of ideas and write an absolutely stellar ending for this thing!

Fox made the long flight back to Corneria. He confirmed the team’s location and entered the atmosphere. He found Falco flying lead formation with Krystal and Slippy over a mountain range.
“This is Fox, reporting in,” Fox said over the com unit.
“Look who decided to show up,” Falco blurted out, “Thought you weren’t coming. Thought you were on your precious vacation.”
“Gimmie a break, Falco. Dinosaur Planet’s current orbital position is on the other side of the system. Now, what’s this about a giant Pokemon?”
“You need to see this for yourself. According to the radar, it’s just over that mountain.”
The team passed over the summit, and Fox could hardly believe what he saw sweeping through the valley.
“It’s a Rayquaza! Like from Brawl, except… enormous! How did it get here?”
“I don’t know. We’ve been following it around for hours,” Falco said, “It rips up the land, then takes off flying for hundreds of kilometers, then it starts ripping up the land again.”
“There’s something strange about its behaviour,” Krystal mused, “I sense that it’s…confused…frustrated. Perhaps searching…”
“We need to subdue it before it starts trashing a city or something,” Falco said, “So far, our lasers have had no effect except to tick it off.”
“Look out!” Slippy yelled.
The Rayquaza had dug a large boulder out of the ground and hurled it towards the Arwings. The group narrowly dodged it. The Pokemon swooped across the valley where it began uprooting trees. It finally moved down near a small lake where it burrowed into the ground, leaving a gaping hole. It stayed there for several minutes.
“I think we’d better check this out,” Fox said, “Krystal, you and Slippy stay in the air in case it comes back out. Falco and I are going to land for a closer look.”
“Roger, Fox!” Krystal replied.
They sat their Arwings down near the hole. Fox and Falco hopped out of their cockpits and walked to the edge. Looking into it revealed only darkness.
“Wherever it’s gone, it’s gone in deep,” Fox said.
“Boy, I’m glad you came all the way across Lylat to deliver these astute observations,” Falco said with a sharp edge of sarcasm.
“Quit busting my chops! You don’t always have to be such a loner, you know! Is it really that bad that you might have to share a bounty with a few teammates?”
“What are you talking about, Fox? If I wanted the bounty for myself, I wouldn’t have made Peppy call you guys out here. But I guess you were more concerned about your stupid vacation.”
“Wait a second. You told Peppy to call me?”
“That’s right. I spotted the Rayquaza myself and quickly realized I was in over my head. I may be a loner, but even I’m smart enough to know when I need help.”
Fox paused for a moment, realizing his mistake. “I…I apologize, Falco. I though that… Never mind.”
“Pfft! Thought you knew me better than that,” Falco said, rolling his eyes. He waved his wing towards the hole. “Now what about that thing?”
Fox rubbed the back of his neck. “Well, it’s gotta come up for air sometime. Maybe we can concentrate our fire into its open mouth. That’s probably its weak point.”
“How do you figure that?”
“Isn’t that always the case?”
Another voice entered the conversation behind them. It was deep and sinister, but familiar. “You’ll never subdue it that way,” it said.
Fox and Falco both spun around and simultaneously exclaimed, "Lucario!”