Tails was alone on the bridge.
"There seems to be a problem with the security system." he said. "Hopefully we'll all have plenty of time to rest up. Since there aren't any Metarex around, things should stay pretty quiet."
Unaware of a dark figure zipping by behind him. Then the figure eyes one of the doors - specifically, the door to Cosmo's room. The Seedrian was sleeping. She opened the door. The shadow unmistakably belonged to Sonic 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 rousing Amy and Cream, and getting the attention of Shadow 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 Sonic standing over her. The red glow stopped.
"You traitor!" Sonic said while she stared in shock and terror.
Knuckles appeared in the doorway and turned the light on.
"Cosmo!" he said then was shocked to see Sonic there.
Sonic threw a Chaos Spear at him, but Shadow immediately arrived and tackled her out of the way. Sonic continued to proceed toward Cosmo, but the battered Sonic stopped him.
"Hold it, Sonic! What is this all about?" he asked and Sonic 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.
"Shadow!" he said.
"Hurry! Grab Cosmo and run!" Shadow said and leapt back, then ran toward Sonic, but rebounded across the ceiling and into her from behind, sending her running down the hall.
Cosmo approached the doorway, fear in her eyes.
"Cosmo, what happened?" Tails asked.
"I woke up... Sonic was there... She said something strange to me..." Cosmo said.
Sonic emerged from the smoke. Tails typed in a lockdown code and ran down the hall with Cosmo. A door shut between him and Sonic. Unfortunately to their surprise, it was no obstacle for her, and she easily broke it down and walked after the fleeing pair. Shadow was left injured on the floor.
'Doctor made you hard to fight!' he thought. 'Where did the old Sonic go?'
Meanwhile Knuckles was running down the hall.
"Shadow, can you hear me! What's going on?" he asked on comlink.
"Shadow got hurt in a fight with Sonic!" Cream said over the comlink.
Meanwhile Cream, Cheese, and Amy were in the infirmary. Amy was watching over Shadow 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."
Elsewhere on the Blue Typhoon.
"For some reason, Sonic was trying to attack Cosmo!" Cream said over the comlink.
"So she is our enemy now!" Knuckles said over the comlink.
Then Amy cut in front of Cream.
"Don't even think about going after Sonic 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 Sonic!" he said on the comlink.
'I'm sorry Sonic.' he thought.
In the Corridors Sonic 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.
She 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 Sonic has access to our computer, she could use the internal sensors to track us. I have to block her from accessing the data." Tails said trying not to cry then hit a button Tails shutting down the heat source search. "That should do it."
Then Sonic's screen went black.
"I think it worked." Tails said while Sonic tried another option on her device.
"Bypass code Six-Delta-Three." the device said and the surveillance camera turned on Tails and Cosmo.
"No way! She got through!" Tails said.
Sonic ran 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.
'What happened to you Sonic?' he thought with a few tears going down.
Meanwhile Sonic was surprised to see that the surveillance screens were empty. No one was to be seen. Suddenly Knuckles punched through the wall.
"Sonic, pick on somebody your own size!" he said and Sonic smirked.
Meanwhile Tails and Cosmo were crawling through the air ducts.
"Why is Sonic against me?" Cosmo asked.
"Maybe Eggman sent her to get you. It's even possible that Sonic's working for the Metarex." Tails said causing her to stopped in surprise.
"The Metarex?!"
"Anyway, it doesn't matter who gave her the orders. Either way, after what she's been doing her whole life Sonic isn't gonna give up until she finishes what she started. But I don't want you to worry, Cosmo. I promise everything will be okay. Because if Sonic tries to hurt you..." he said and paused before turning around. "...she'll have to get past me first!"
"Thank you..."
Meanwhile in a corridor Sonic rained Chaos Spears at Knuckles as the she ran toward him. Knuckles tried to land a punch on her, but she teleported behind him and Chaos Spears a pipe, creating a mist that blinded him. This was her 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 Sonic emerged from the smoke.
"Hand that girl over now. I don't want to fight you, Tails, but I will if I have to." Sonic said.
"Cosmo never did anything to harm you! Why are you after her anyway?" Tails said.
'Maybe there's still a part of the old Sonic in her!' he thought hearing she doesn't want to fight him.
"I'm not going to tell you." Sonic said. "Now move aside or you'll be sorry." she said darkly.
"Forget it, Sonic! I won't let you hurt Cosmo!"
"...I'm warning you." she 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 Sonic to help her 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 Sonic can communicate, can't you?"
She nodded.
"Does that make you feel jealous?"
"Call her 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 Sonic. "Sonic, come in. It's Rouge." she said on the radio.
In the Hanger Sonic beard down on the X-Tornado. Her radio was lying on the ground.
"Sonic, do you read me? Come in, Sonic. Is something wrong?" Rouge asked over the radio.
In the Corridor.
"Sonic, why aren't you answering? Sonic! Sonic!" Rouge said on the radio. "It's no use. She's not responding." she said off the radio.
"I hope Tails and Cosmo are all right..."
In the Hangar.
"Back off, Sonic, or I'll have to stop you myself!" Tails said and Sonic stopped and smirked.
"Don't be a fool! I'm too powerful!" she said. "I'm twice as strong as Shadow and at least I'm not Super or Dark Sonic."
"Yeah? Well, I got the X-Tornado!" Tails said and converted to X-Cyclone and moved forward, but Sonic 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 propelled 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 Sonic left the wreckage.
She 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. Sonic leapt up the shaft, accidentally touching a laser.
"Intruder alert. All stun lasers fire on target." Mainframe said.
Even with security lasers firing at Sonic, she was still able to dodge them. Cosmo saw her coming.
"Here she comes!" she said.
"It's okay. Just trust me." Tails said.
There was fear in Cosmo's eyes and determination in Tails'. Sonic destroyed the security lasers with Chaos Spears as she 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. Sonic saw the door in the ceiling close. She ran into it before falling down to a pipe below.
"Come on, Cosmo!" Tails said and they run down the small corridor, but Sonic broke through the door and spun toward them.
Suddenly Knuckles showed up and held Sonic back.
"It's Knuckles!" Cosmo said.
"Get outta here quick!" Knuckles said straining Sonic.
Sonic started to push him back.
"Please Sonic, I don't want to hurt you!" he said and used his brute strength to throw her through the ceiling. "Go! Now!"
"Be careful, Knuckles." Tails said as Sonic emerged from the hole.
'We're sorry Sonic.' he thought.
"Trying to challenge me is a big mistake, and you are going to regret it Knux." Sonic said.
"I've always wanted to sonbox!" Knuckles said.
"As you wish." she said and rebounded off the four surfaces of the hall toward him.
Then she 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! Sonic 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, Sonic. 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 Sonic arrived and stood in front of them. "...but I won't tell you what it is." she 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 fighting tears and threw the switch, and a door lowered between them.
"Do you seriously believe a door can stop me?" Sonic asked amused.
"Maybe you're not as strong as you think." Tails said and the door closed.
"This will be too easy." Sonic said and tried to Chaos Spear the door down, but to no effect.
Suddenly she felt an electric current run through her, and felt the ground under her rising. She rose up into the barrel of the Shadow Driver.
"I'll spin free!" she said and spun in a ball as the Shadow Driver was activated.
"Sonic fell right into my trap. Activate Shadow Power Cannon now!" Tails said and pulled another switch, and the Shadow Driver fired Sonic out into space.
Tails panted from the adrenalin.
"We lucked out, Cosmo." he said and turned around. "Sonic 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 Sonic went to space." Cream said over the comlink.
"Way to go, buddy." Knuckles said.
"Where's Sonic?" Rouge asked.
"She's gone now. Tails was able to use the Shadow Power Cannon to send Sonic 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 Sonic. You should know that after working with her for so long."
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 Sonic Chaos Controlled in front of them, white Chaos Emerald in hand. The Emerald fell apart.
"This Emerald is a fake." she said.
"Let's settle this now!" Tails said and charged toward Sonic, but she punched him aside.
"He's hurt!" Cosmo said as Sonic started toward her.
Tails got back up and leapt onto Sonic from behind, but she threw him into the command chair's stairs and collapsed.
"What have I done...?" Cosmo asked then gasped, and her eyes shrunk in fear as Sonic turned back to her.
Soon Sonic had her at her 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 Sonic's leg.
"Leave her alone... If you don't, you'll be sorry!" he said weakly and tears going down seeing what Sonic is now.
Sonic smirked, knowing Tails wasn't able to do anything. She was about to return to her 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.