Disclaimer (because I forgot it in Chapter 1): You know the drill. The only thing in this story that I own is the way I put stuff. The characters, the locations, and even the storyline (!) are owned by some SEGA-related company.

Chapter Two: Stowaway! (The actual Metroid-related part)

Sub-Chapter 1: Last Ditch Attempt

Sonic knew that this would be his last chance to meet Samus. Ever. So after the photo shoot, he ran away and hid out near Samus's ship. He knew that the gang would be worried, but he didn't care. When Samus came and opened the gate into the ship, Sonic climbed in at the speed of sound. He noticed the TV, hiding behind it, at first missing the Dreamcast. He felt the shock of lifting off, then saw Samus do something. Making sure she was light-years away from Mario's planet, she happily booted up the Dreamcast. That's when Sonic saw it. The game. A mint-condition, carefully preserved, temperature-controlled copy of...Sonic Adventure? This can't be right, Sonic thought. Why would she have a copy of my game aboard her ship? Unless... Sonic pondered. Unless she's as obsessed with my games as I am with hers.

The tournament is over until tomorrow, Samus thought. Now I can relax and play Sonic Adventure. And, best of all, NO INTERRUPTIONS! Everyone will think I'm busy training so they won't bother me. Her reveling was interrupted by the sounding of a very loud alarm, something like her phone ringing; sometimes it took a lot to break Samus out of her games. She picked up the phone, only to hear a dial tone. The alarm continued, so apparently no one was calling her. That's when she saw a huge dragon swooping at her. "Ridley!" a voice screamed. But it wasn't Samus's. Without realizing it, Sonic had screamed, out of either excitement or fear, at the sight of the boss monster that he could easily recognize, having fought it so many times. It flew down to the surface of a planet that Samus (and Sonic) would have recognized as Zebes, if they hadn't both known that the planet was destroyed already. Then they both realized something: it was SR388! If the Space Pirates got hold of the many creatures there, or, worse, if even one Metroid had survived Samus's Metroid extermination, the Pirates' presence could mean disaster. Samus took the ship to the surface, forgetting about the disembodied voice from before. Until Sonic made the dumbest move of his life.

Sub-Chapter 2: The New Partner, the New Mission

"SR388? I never thought I'd actually see this place for real! There's even a breathable atmosphere!" Sonic exclaimed, breathing deeply. "Huh? Who was that?" Samus replied. Then she saw Sonic standing behind her with an excited look on his face, completely unaware that he'd just let not only Samus but everyone within 10 miles know where he was (Unfortunately for Tails, he was not within ten miles). That's when Samus took control. "Wait, how'd you know where we are? Unless...you're so busted!" she said, realizing Sonic's secret.

"Yeah, well wait until my buddies find out that you're the Dreamcast Queen!"

"Well, apparently neither of us are going anywhere with each other's secret without revealing ourselves, so I might as well arm you and request your assistance on this mission."

"In English?"

"You're along for the ride."

"Alright!"

With that, Samus dug around her glove box for her emergency pistol, spare helmet, and other tools, such as a wire cutter (you know, in case you get stuck in barbed wire) and a set of mint-condition bobby pins of various sizes (even though the cages and prisons have laser bars instead of metal, they still have the same easy-to-pick locks) and gave them all to Sonic.

Little did they know that they were in for their toughest mission ever.

Samus was quick to assess the situation. "Well, considering I came to the tournament armed with only the Charge Beam, Morph Ball, Bombs, Screw Attack, Varia Suit, and a mandatory shield-generator thing, and I left everything else at home, I've got a lot of searching to do. I hope the Chozos made duplicates1 "

"You mean those bird guys?"

"Yeah."

"They're on this planet too."

"Oh...oh yeah, like in Metroid 2!"

"Now you got it."

"Ok, so I'll tell you if I see any red doors."

"Why?"

"On a planet with no hatches, that usually means a Chozo Statue, and they usually mean items."

"Ok."

"Oh, and one more thing."

"What?"

"Can I have the duplicate items we find?"

"Yeah, sure."

"Alright!"

Sub-Chapter 3: First Upgrade—Sonic's Morph Ball

Since Samus knew the local terrain so well and knew she'd need to teach Sonic everything she knew, she landed in her original landing spot. They found one difference, though.

"A Morph Ball? I don't remember this here. I thought I started Metroid 2 with Morph Ball."

"Maybe you dropped it."

"Well, it doesn't make much sense, but that explains why I started Super Metroid without it. Anyway, I have one, so it's yours now."

"Sweet! One problem; I can already roll up into a ball, but I eventually lose speed and unroll. Maybe with this, I can stay super-small and super-fast forever."

He tried it and it didn't work.

"Well, maybe you can only use things like bombs when you have that," Samus suggested.

"Eh, you're probably right. Might as well wait for those. You said you had some already, right?"

"Yeah."

"So I can have any we find?"

"Yeah."

"Sweet!"

With that, they ventured forth into the planet. They found the Chozo ruins untouched; apparently the Pirates had landed somewhere else. And there were more items, so apparently the Chozo still existed somewhere. Sonic and Samus were both well pleased by the results: replacement Ice Beam, Wave Beam, Plasma Beam, Spring Ball, High Jump, and Missiles for Samus and a Varia Suit, extra Missiles, Screw Attack, Space Jump2, and Bombs for Sonic. Plus, Sonic found a job. Since he could defeat enemies by spinning, Samus could use him as a spinning shield.

Sub-Chapter 4: Lack of Evidence

In about an hour, Sonic and Samus had covered the entire area of SR388 that Samus had previously explored, and they found no trace of Space Pirates.

"Well, that was uneventful," commented Samus.

"Yeah, usually..." Sonic started, but he was cut off at the sight of something shocking. They had just crossed the room where the Queen Metroid had stood when they noticed something: a bubble door just beyond the exit. This could only mean one thing...

1For those unfamiliar with the Metroid games, Samus was orphaned as a young child by a Space Pirate attack on her colony on Zebes. An ancient, intelligent, bird-like culture called the Chozo then found her and realized that they must raise her and train her in the ways of combat if she is ever to protect herself. They were also skilled builders and technicians with futuristic weaponry, and they were actually solely responsible for creating every weapon Samus had ever used. Thus, here she expresses hope that she can find replacement weaponry.

2Judging by Samus's jumping actions in SSB, she apparently has Space Jump in that game.