Chris and Tails were alone on the bridge. Chris stretched.
"Hey Tails, don't you think it's time we took a break?" Chris asked.
"Well... there seems to be a problem with the security system and I wanna find out why. But you can go." Tails said.
"Don't you want help?"
"Nah, I can handle it myself. Hopefully we'll all have plenty of time to rest up. Since there aren't any Metarex around, things should stay pretty quiet."
"I sure hope you're right, Tails."
"Me too."
Then Chris yawned, stretched, and headed to his room, unaware of a dark figure zipping by behind him. When he was gone, the figure eyes one of the doors - specifically, the door to Cosmo's room. The Seedrian was sleeping. He opened the door. The shadow unmistakably belonged to Shadow the Hedgehog.
On the bridge.
"Okay, that should work. Now I'll restart the system." Tails said and pressed a button.
Suddenly an alarm went off, bathing the ship in a red glow and startling Chris at his desk, and rousing Amy and Cream, and getting the attention of Sonic and Knuckles.
"Red alert! Red alert! We have an intruder on board the ship!" Tails said over the intercom.
Back in Cosmo's room Cosmo awoke to see Shadow standing over her. The red glow stopped.
"You traitor!" Shadow said while she stared in shock and terror.
Chris appeared in the doorway and turned the light on.
"Cosmo!" he said then was shocked to see Shadow there.
Shadow threw a Chaos Spear at him, but Sonic immediately arrived and tackled him out of the way. Shadow continued to proceed toward Cosmo, but the battered Sonic stopped him.
"Hold it, Shadow! You mind tellin' me what this is all about?" Sonic said and Shadow beard down on him.
They clashed in the hall. Neither of them able to get the upper hand in the grudge match. Then Tails ran in.
"Sonic!" he said.
"Hurry! Grab Cosmo and run!" Sonic said and leapt back, then ran toward Shadow, but rebounded across the ceiling and into him from behind, sending him rocketing down the hall.
Cosmo approached the doorway, fear in her eyes.
"Cosmo, what happened?" Tails asked.
"I woke up... Shadow was there... He said something strange to me..." Cosmo said.
Shadow emerged from the smoke. Tails typed in a lockdown code and ran down the hall with Cosmo. A door shut between him and Shadow. Unfortunately, it was no obstacle for him, and he easily broke it down and walked after the fleeing pair. Chris and Sonic were left injured on the floor.
Meanwhile Knuckles was running down the hall.
"Sonic, can you hear me! What's going on?" he asked on comlink.
"Sonic and Chris got hurt in a fight with Shadow!" Cream said over the comlink.
Knuckles was worried now.
Meanwhile Cream, Cheese, and Amy were in the infirmary. Amy was watching over Sonic, Cheese over Chris, and Cream was speaking to Knuckles.
"They'll be okay, but it'll take some time for them to recover." Cream said.
"Why were they fighting?" Knuckles asked over the radio.
"It's really confusing."
They all knew he was worried now.
Elsewhere on the Blue Typhoon.
"For some reason, Shadow was trying to attack Cosmo!" Cream said over the comlink.
"So he is our enemy!" Knuckles said over the comlink.
Then Amy cut in front of Cream.
"Don't even think about going after Shadow right now! Find Tails and Cosmo and make sure they're safe! That's an order!" she said over the comlink.
"Leave it to me! It's dangerous, so you stay put!" Knuckles said. "I know what I'm doing! Nobody'll be safe on this ship 'til we stop Shadow!" he said on the comlink. "And I'm not letting him hurt my best friend again!"
In the Corridors Shadow broke down another door and scanned the halls before pulling out his cellular device.
"Accessing ship's internal sensors. Two heat signals detected. Stand by for visual." the device said.
He saw the heat signature of Tails as he worked on a computer in another hall. Cosmo was with him.
"What are you doing, Tails?" Cream asked.
"If Shadow has access to our computer, he could use the internal sensors to track us. I have to block him from accessing the data." Tails said then hit a button Tails shutting down the heat source search. "That should do it."
Then Shadow's screen went black.
"I think it worked." Tails said while Shadow tried another option on his device.
"Bypass code Six-Delta-Three." the device said and the surveillance camera turned on Tails and Cosmo.
"No way! He got through!" Tails said.
Shadow skated down the hall as Tails and Cosmo broke into a run. The security doors closed behind them.
"Hurry, Cosmo!" Tails said as his grip on Cosmo's hand tightened.
Meanwhile Shadow was surprised to see that the surveillance screens were empty. No one was to be seen. Suddenly Knuckles punched through the wall.
"Shadow, pick on somebody your own size!" he said and Shadow smirked. "You've done enough to Sonic last time. Even though you helped us!"
Meanwhile Tails and Cosmo were crawling through the air ducts.
"Why is Shadow against me?" Cosmo asked.
"Maybe Eggman sent him to get you. It's even possible that Shadow's working for the Metarex." Tails said causing her to stopped in surprise.
"The Metarex?!"
"Anyway, it doesn't matter who gave him the orders. Either way, Shadow isn't gonna give up until he finishes what he started. But I don't want you to worry, Cosmo. I promise everything will be okay. Because if Shadow tries to hurt you..." he said and paused before turning around. "...he'll have to get past me first!"
"Thank you..."
Meanwhile in a corridor Shadow rained Chaos Spears at Knuckles as the he ran toward him. Knuckles tried to land a punch on Shadow, but he teleported behind him and Chaos Spears a pipe, creating a mist that blinded him. This was Shadow's opportunity to escape.
"Come back here!" Knuckles said.
There was another figure behind him. Knuckles was shocked to see that is Rouge.
"Are all redheads as temperamental as you?" Rouge asked.
In the Hangar.
Tails and Cosmo crept toward the X-Tornado and climbed the ladder.
"You'll be safe once we get away on the X-Tornado." Tails said and typed his identity into the touch screen. "Prepare for takeoff! Hold on, Cosmo!" he said and the catapult system was engaged. "Everything will be okay."
Suddenly an explosion ensued in front of them and Shadow emerged from the smoke.
"Hand that girl over now. I don't want to fight you, Tails, but I will if I have to." Shadow said.
"Cosmo never did anything to harm you! Why are you after her anyway?" Tails said.
"I'm not going to tell you." Shadow said. "Now move aside or you'll be sorry." he said darkly.
"Forget it, Shadow! I won't let you hurt Cosmo!"
"...I'm warning you." Shadow said and Cosmo cowered behind Tails' seat. "This is your last chance, Tails. Give up now or face the consequences."
In a corridor.
Knuckles and Rouge stared each other down.
"Well? What are you here for?" Knuckles asked.
"Strain your brain and guess." Rouge said.
"Are you working with Shadow to help him attack Cosmo?"
"Bingo. You're not as dimwitted as you look."
"Why are you doing this?"
"I'm surprised you and your spaced-out crewmates haven't figured that out for yourselves. That girl Cosmo's a real plant... in more ways than one."
"I'm not kidding around, Rouge! You and Shadow can communicate, can't you?"
She nodded.
"Does that make you feel jealous?"
"No! I'm not jealous, I'm fine with my girlfriend not you! Now call him now, or I'll knock that smirk off your face!"
"No need to be pushy." she said frustrated then pulled out her device and contacted Shadow. "Shadow, come in. It's Rouge." she said on the radio.
She could tell that he and Sonic are both having trouble controlling themselves for some reason still.
'Sonic has to have been doing something with Knuckie for a long time. If he left his girlfriend they must be very close and Sonic must have left someone to. I wonder if he has a girlfriend and left her?' she thought.
In the Hanger Shadow beard down on the X-Tornado. His radio was lying on the ground.
"Shadow, do you read me? Come in, Shadow. Is something wrong?" Rouge asked over the radio.
In the Corridor.
"Shadow, why aren't you answering? Shadow! Shadow!" Rouge said on the radio. "It's no use. He's not responding." she said off the radio.
"I hope Tails and Cosmo are all right..."
In the Hangar.
"Back off, Shadow, or I'll have to stop you myself!" Tails said and Shadow stopped and smirked.
"Don't be a fool! I'm too powerful!" he said.
"Yeah? Well, I got the X-Tornado!" Tails said and converted to X-Cyclone and moved forward, but Shadow Chaos Speared the left leg off sending the vehicle falling onto its side, cracking the canopy.
Then he sped Cosmo away from the wreckage with his namesakes as the X-Cyclone propeled itself towed shadow and exploded.
In the Corridor.
"Something just blew up in the hangar!" Rouge said over the radio.
"I've gotta reach Tails before it's too late." Knuckles said.
In the Hangar the automatic sprinkler system turned on as Shadow left the wreckage.
He spotted an elevator shaft. Tails was flying Cosmo up the shaft, which is guarded by infrared security lasers. Tails was wearing an infrared scope so he saw the lasers. Shadow leapt up the shaft, accidentally touching a laser.
"Intruder alert. All stun lasers fire on target." Mainframe said.
Even with security lasers firing at Shadow, he was still able to dodge them. Cosmo saw him coming.
"Here he comes!" she said.
"It's okay. Just trust me." Tails said.
There was fear in Cosmo's eyes and determination in Tails'. Shadow destroyed the security lasers with Chaos Spears as he rebounds up the walls. Tails glanced at Cosmo.
"Almost there!" Tails said as they entered a shaft in the ceiling.
Then he mashed an emergency button as they rolled to a stop. Shadow saw the door in the ceiling close. He ran into it before falling down to a pipe below.
"Come on, Cosmo!" Tails said and they run down the small corridor, but Shadow broke through the door and spun toward them.
Suddenly Knuckles showed up and held Shadow back.
"It's Knuckles!" Cosmo said.
"Get outta here quick!" Knuckles said straining Shadow.
Shadow started to push him back.
"I've had enough of you, Shadow!" Knuckles said and used his brute strength to throw Shadow through the ceiling. "Go! Now!"
"Be careful, Knuckles." Tails said as Shadow emerged from the hole.
"Trying to challenge me is a big mistake, and you are going to regret it." Shadow said.
"I've always wanted to shadowbox!" Knuckles said. "Especially after what you did to Sonic!"
"As you wish." he said and rebounded off the four surfaces of the hall toward Knuckles.
Then he slammed backward and landed on the floor.
Meanwhile, Tails and Cosmo ran through a door.
"Ah! It's a dead end! We have to find another way out!" Tails said.
Suddenly it exploded behind them.
"Come on!" he said.
They made a right, and were forced to stop at a dead end. There was a control panel there.
"Please hurry! Shadow will catch up with us soon!" Cosmo said.
"Sooner than you think." someone said.
They saw a shadow approaching.
"I guess this is it." she said and Tails stood protective in front of her. "Wait a second, Shadow. If you insist on getting rid of me, you should at least tell me the reason why."
"I do have a reason..." they said as Shadow arrived and stood in front of them. "...but I won't tell you what it is." he continued and slowly approached them, not knowing that Tails' hand was on a switch. "There's no point in putting up a fight because you can't beat me."
"You don't have to do this." Cosmo said.
"You won't talk me out of getting rid of you, so don't try!"
"Stay back! I won't let you near her!" Tails said and threw the switch, and a door lowered between them.
"Do you seriously believe a door can stop me?" Shadow asked amused.
"Maybe you're not as strong as you think." Tails said and the door closed.
"This will be too easy." Shadow said and tried to Chaos Spear the door down, but to no effect.
Suddenly he felt an electric current run through him, and felt the ground under him rising. He rose up into the barrel of the Sonic Driver.
"I'll spin free!" he said and spun in a ball as the Sonic Driver was activated.
"Shadow fell right into my trap. Activate Sonic Power Cannon now!" Tails said and pulled another switch, and the Sonic Driver fired Shadow out into space.
Tails panted from the adrenalin.
"We lucked out, Cosmo." he said and turned around. "Shadow started spinning at just the right time. You should be safe now." he said and Cosmo nodded. "Let's go."
Cosmo took his hand. Meanwhile, Rouge was tending to Knuckles on the floor of the hall.
"It's okay. Tails said Shadow went to space." Cream said over the comlink.
"Way to go, buddy." Knuckles said.
"Where's Shadow?" Rouge asked.
"He's gone now. Tails was able to use the Sonic Power Cannon to send Shadow on a long trip. And you're next..." he said and sat up. "...unless you tell me what's goin' on!"
"Your foxy friend just make a huge mistake." she said and produced the device Leon gave her. "Cosmo is the real enemy, not Shadow."
On the Bridge Tails and Cosmo were standing at the upper deck together.
"I'm sorry I'm causing you so much trouble." Cosmo said.
"You don't have to apologize, Cosmo. You mean a lot to me, and the only thing I care about is making sure you're safe." Tails said.
There was a long pause as they looked at each other. Then they headed to their posts. Suddenly Shadow Chaos Controlled in front of them, white Chaos Emerald in hand. The Emerald fell apart.
"This Emerald is a fake." he said.
"Let's settle this now!" Tails said and charged toward Shadow, but he punched him aside.
"He's hurt!" Cosmo said as Shadow started toward her.
Tails got back up and leapt onto Shadow from behind, but he threw him into the command chair's stairs and collapsed.
"What have I done...?" she asked then gasped, and her eyes shrunk in fear as he turned back to her.
Soon he had her at his mercy.
"Let's get this over with." he said.
Just as he was about to deliver the finishing blow, Tails used the last of his energy to grab on to Shadow's leg.
"Leave her alone... If you don't, you'll be sorry!" he said weakly.
Shadow smirked, knowing Tails wasn't able to do anything. He was about to return to his business when a hole was blasted in the giant canopy above them. Glass rained down as a black blur speeds in, destroyed Tails' console at his command chair, and sped back out as various objects were sucked into space. Cosmo held onto the railing for dear life. Her grip slipped, but Tails grabbed on to her. Four balls of protective webbing sealed the hole, and the suction stopped. Tails and Cosmo collapsed on the ground as a gigantic ship, Dark Oak's Battleship, pulled up next to the Typhoon.
On Dark Oak's Battleship.
"Well done, Cosmo, or should I say, White Seed." Dark Oak said.
On the Blue Typhoon Bridge Cosmo was shocked.
"You have now completed your mission." Dark Oak said.
Cosmo has a feeling of fear and dread.
"White Seed. Mission. What mission? What is he talking about?" she said to herself.
Cosmo cowered as the Scarship overshadowed her. One of its missiles struck the bridge of the ship. She ran down the hall.
An explosion rocked the side of the ship near her.
"It's too late... The Metarex are coming..." she said when a red-eyed Metarex turned toward her.
"If you want to survive, then listen to me. Pay close attention." Dark Oak said on voiceover.
"Don't... Don't listen..."
Back on the Bridge.
"From now on, you will report everything to me. Your eyes will be my eyes. Your ears will be my ears. You will be the ultimate spy. Your codename will be White Seed." Dark Oak said on the voiceover.
Suddenly Cosmo's amulet started to glow and she screamed.
The Blue Typhoon, then Dark Oak's Battleship, were bathed in an intensely bright glow. Then they vanished.