Meanwhile, back in Altea, Luigi was still in Zelda's room. He had rarely left the room, only occasionally to eat, and to use the bathroom. He was in there so often, that usually, Shadow would leave him a plate of food. Luigi usually only took two or three bites of the food in his plate, then one of the workers in the castle would take the barely touched meal away. In the time he'd been in there, Zelda had yet to regain consciousness. By now, he hadn't bathed, so he smelled. He could feel how nasty his teeth felt. He was also starving, which was his fault. And he hadn't slept that much. His eyes were red and slightly bloodshot.
"Maybe that's why Zelda isn't waking up. I probably look and smell atrocious," Luigi thought to himself, even smiling for a moment. But he was eventually back to wallowing in his own misery. That was when Shadow stood in the doorway.
"Luigi, you need to come out of there. You're worrying everyone. Besides, I've got to show you some of the stuff I've found when I was researching," Shadow said. Luigi felt torn now. For one, he didn't want to leave Zelda's side. But he also wanted to eat something. Plus, he knew that he needed to get himself cleaned up.
"Alright, but first, I need some food and a shower."
20 minutes later, Luigi sat in the library, now cleaned up, with a fresh shirt and pair of overalls, and now eating a sandwich. Shadow took out his notes from the book on the Power Glove. He handed the notes to Luigi.
"What's this?"
"Some notes I took. That way you don't have to read this book. Just read it," Shadow answered. Luigi read through Shadow's notes for a couple minutes. He set the notes back down on the table, taking a bite of his sandwich.
"So, Waluigi got this Power Glove and is trying to find these stones for it. So what?" Luigi shrugged. That was when Shadow held up the Time Stone. Luigi dropped the crust of his sandwich.
"W-w-w... where did you get that?" Luigi stammered.
"I got it from Robin. Robin got it from Zelda. Zelda somehow got the Time Stone. That's why Waluigi attacked her," Shadow explained. Luigi went pale. He sat staring at the green stone in Shadow's stone. He felt the pieces of the puzzle starting to come together. That was when Mario, Falcon, Ryu, and Ken entered through a portal into the library.
"Hey Shadow, Luigi. Falcon, can you show these two around?" Mario asked.
"Yes! Come on gentlemen, follow me!" Falcon said, leading the two out of the library.
"Luigi! Nice of you catch a few rays!" Mario joked. Luigi didn't respond. Mario raised and eyebrow.
"What's with him?" Mario asked Shadow, realizing Luigi's pale frame.
"I just told him everything I've gathered. He's not taking it well," Shadow said. That was when Luigi stood up, pounding his fist on the table.
"Where to next?" Luigi asked, color returning to his face. He took a bite to the other half of his sandwich.
"Well, it's actually kind of random... why?"
"I'm coming. I'm making sure anyone associated with Waluigi will pay," Luigi said boldly.
"OK... the faster we go back and forth, the more we can recruit."
"I'll come too. My research is done. And I'll make sure what happened to Sonic, doesn't happen to me," Shadow spoke up.
"Wait, what happened to Sonic?" Luigi asked.
"We'll talk about that later. Let's get going," Shadow said. Mario set up the device to another random coordination, and the three took off. When they arrived, they saw themselves in unfamiliar territory. The place looked very futuristic.
"Now what?" Mario asked.
"Has this been happening every time you've done this?" Shadow asked.
"Well, except for Falcon. But let's find where we're at. And where to go," Mario said. They started going, but were stopped by the giant robot landing in front of them.
"Whoa! Where'd that thing come from?" Mario yelled, diving out of the way of a laser from the robot.
"I did!" A voice said. The three looked up to see a man in a ship. He wore a white robe, and had crazy hair. He had crazy eyebrows and a crazy look on his face.
"Who are you?" Luigi asked.
"I am Dr. Wily. The greatest scientific genius in the world," Wily said before laughing. That was when more robots surrounded the three.
"You're surrounded. Give up! If you surrender now, I'll be sure to let the Emperor know to spare you," Wily cackled.
"Wow, Waluigi now has the guts to call himself emperor," Luigi said.
"Or, I could just get you out of the way now. I like that idea better. Farewell!" Wily laughed, as the robots closed in.
"I don't think so, Wily!" said the voice that sounded like a young man. As the robots fired their weapons, a boy in blue put up a shield, blocking the oncoming attacks. He then sent the leaves out at the robots, destroying them. It was the Blue Bomber, Megaman!
"Hey, Mario! Long time no see!" Megaman said.
"Light, you old coot! Why must you always send your toys to destroy my creations?" Wily said angrily, pounding his fists.
"Well, you're all alone, Wily. You're going down!" Megaman said, as Wily began to fly away. Mario, Luigi, and Shadow began to follow behind.
"Not so fast, Shadow!" Said another voice. Shadow stopped and whirled around to see Doctor Eggman approaching in his Egg Mobile.
"Eggman. I almost missed your chrome dome," Shadow said grimly. He prepared for battle.
"Why so keen to join your friends? Speaking of which, I have an old friend for you to see," Eggman said, pushing a button at the control panel. This cause Metal Sonic to suddenly fly up in front of Shadow. His design looked slightly different.
"Metal Sonic? Come on Eggman, I've kicked his tin can around so many times. What's going to be different this time?" Shadow asked with a smirk.
"Oh, you'll find out," Eggman answered, pulling out a remote control. He then pushed a button. Metal Sonic's head snapped up.
"Metal Sonic prototype number fourteen," Metal Sonic said in a robotic voice. Shadow stopped. Metal never talked before. And the one time he did, he didn't sound anything like that.
"Mission objective: destroy Shadow the Hedgehog," Metal Sonic said. Shadow's eyes went wide. He knew that voice anywhere. Everything was coming together. And he felt like throwing up.
"Well, I see you're understanding now," Eggman said,  caressing his mustache.
"You turned Sonic into a robot?" Shadow demanded. He felt his angry overflowing within himself.
"Well, it's more of a cyborg. But you get the idea. I'll leave you with your friend. I'm sure you've got catching up to do. Have fun Metal! You too Shadow!" Eggman laughed as he headed off to catch up with Dr. Wily.
"Destroy Shadow the Hedgehog," Metal Sonic said again. He charged up a spin dash, launching himself at Shadow. Shadow quickly teleported out of the way.
"I can't believer he did this to you!" Shadow shouted.  He quickly launched multiple Chaos Spears, but as the approaches Metal, he shot rockets to deflect them.
"He gave you rocket launchers??? At least that much is cool," Shadow replied. Metal approached Shadow, and the two began to battle hand-to-hand. Metal definitely had the fighting skill of normal Sonic.
"You may match Sonic in strength, but how about speed?" Shadow asked. He quickly turned and sprinted in the direction that Eggman went. Metal followed. The two kept on even pace. He two both took turns attempting to home attack each other each missing. Shadow eventually jumped up for a Chaos Spear, Metal home attacked, knocking Shadow to the ground. Metal then sent more missiles toward the dark hedgehog. Shadow barely had time to make a shield out of chaos energy to block. Shadow fell to one knee. Metal approached, ready to finish the job.
"Huh. You're not so bad. But there's one thing you forgot; the original always superior. CHAOS CONTROL!" Shadow yelled, holding one of the Chaos Emeralds up, freezing every thing. Quickly, Shadow used quick attacks to knock Metal off guard. Then he launched Metal up in the air, teleported above Metal, then dropped him with an axe kick. Just before Metal landed, Shadow teleported below him. He let his anger let loose.
"Chaos... BLAST!" Shadow yelled. When the blast cleared, Metal was down. Under too much stress, Metal had shut down. Shadow went up to Metal Sonic. His friend, now just tin can. Shadow pounded his fist into the ground.
"I could've stopped this... none of this would have happened...," Shadow thought to himself. He was still thinking about it when he heard his friends.
"Shadow!" Shadow turned to see Mario, Luigi, and Megaman.
"Did you get Wily and Eggman?"
"They escaped in one of those portals before we could catch them. Sorry."
"Figures, those cowards."
"Wait, whose the tin can?"
"Oh, that's Metal Sonic. It's a clone of Sonic made by Eggman. Though it's a little more than a clone this time...," Shadow said.
"Wait, what do you mean?" Mario asked. Shadow told the three about how Eggman had turned Sonic into a cyborg. Mario and Luigi looked in shock.
"Whoa... that Eggman is crazy..."
"What they did to him is disgusting," Shadow said, shaking his head.
"Well, what do we do? Can't we turn him back on or something?"
"He'd still be crazy and try to attack us."
"Maybe we can recalibrate his wires or something. At least give him his own will back," Megaman suggested.
"Would that work? Who would do it?" Shadow questioned.
"One second," Megaman answered. He tapped some buttons on his wrist. A small hologram of an old man appeared.
"Dr. Light?"
"Megaman, my boy! How did the chase of Wily go?"
"He got away, sir. But right now, some friends of mine need help. Can you by any chance come here right now?"
"Sure thing! Give me a second," Light said. After a few minutes, Light appeared in a vehicle similar to Wily's. Megaman showed Light the problem.
"A robot? What happened?" Light said, examining Metal Sonic carefully.
"This is Sonic the Hedgehog. Wily and another mad scientist turned him into a cyborg pretty much. But he's not in his own mind. Is there a way you can fix that?"
"I can try. I have my tools. I can take him to the lab and take care of it there."
"Thank you, Dr., but we don't have time to do it here. We can't fiddle around here forever. We have other things to worry about," Luigi spoke up.
"Well, what about your friend? You're not going to leave him here, are you?"
"Come with us, and you could work there. They might not be the greatest are to work, but you should have enough time to fix him up," Shadow suggested. Dr. Light thought about this. He nodded.
"Okay, I'll see what I can do. Let's go, we don't have time to waste," Light said. Mario set the coordinates to Altea, then Mario, Luigi, Shadow. Megaman, and Dr. Light(with Metal Sonic) headed to headquarters. Shadow was glad his friend was back. But he wasn't sure if he'd ever be the same again.