Amnael's Endgame, Part 1

After regaining consciousness Chazz found himself in a unknown location. He then looked to the side and saw Alexis unconscious.
"Where exactly on Earth are we?" Chazz asked himself.
There was a bright light and he saw Earth in the distance.
"Scratch that, where exactly off Earth are we?"
Back at Duel Academy Jaden, Syrus and Chumley were coming to terms with what was going on.
"So if the other gates have been opened, that can only mean one thing." Chumley noted. "There aren't very many people left." 
"Jaden, you should hide. The final Shadow Rider might look for you so he can unlock the last gate." Syrus pointed out.
"What does that say about Kaoru?" Chumley asked. "She's out there as well."
"Then we gotta find her." Jaden said.
He, Syrus and Chumley ran off to find her before the last Shadow Rider did. 
A second later, a lightning bolt fell from the sky, striking a nearby tree. The boys cried out in surprise and got out of the way as it fell over, splashing into the lake.
"Aw man, that was way too close."
"Hey, look." Jaden pointed at the splintered tree trunk, where the Mark of Amnael was glowing.
The light vanished, then reappeared further away, then moved further back, leading them down a trail in the forest. 
"It's like… it's trying to lead us someplace." Syrus observed.
As they walked through the hallway, lightning flashed outside, the flash and thunder scaring Pharaoh so that he jumped out of Chumley's arms and ran down the hall. "Pharaoh!"
"Aw man!"
"Let's go get him." Syrus and Chumley followed Jaden's lead, going deeper into the abandoned dorm in pursuit of Pharaoh. Eventually they came to the same underground tunnels they'd been through before back when Titan had kidnapped Alexis.
Chumley shivered as they walked through the dark passageway. 
"I'm telling you, this place gives me the creeps. Hey look." Chumley shined his light at a hole in the wall, just large enough for the fat cat to have squeezed through. "And Pharaoh's paw prints."
"Come on, Sy." Jaden said. "Let's keep moving. With any luck we'll find another way in." Despite misgivings, they continued down the tunnel, until eventually they reached a side corridor with a wide open doorway at the end. "Whoa… this is weird."
"This door wasn't here the last time we came to the Abandoned Dorm." Jaden noted.
"Really? Let's check it out."
Despite Syrus and Chumley's misgivings, the boys walked through the doorway and found themselves in a large dark room. Shining their lights around, they saw something big carved into the floor, strange pieces of equipment, and most prominently, three stone tablets against the far wall depicting creatures not unlike the Egyptian God cards. 
"Man, this place looks like some lab from a horror movie." Jaden remarked.
Chumley gulped audibly at this. "So… where's the mad scientist hiding?"
Syrus let out an 'eep' and trembled as he pointed his flashlight at the wall. "If it's where my gut tells me it might be, then I'm gonna need a change of shorts."
Jaden looked where Syrus was aiming his light and saw a coffin propped up against the wall. "A coffin…"
"Maybe it's a refrigerator box." Chumley suggested.
"Yeah, exactly." Syrus agreed. "No need to check it out."
Despite this, Jaden still approached the coffin. "Come on guys, give me a hand here."
"Sorry Jay." Chumley excused himself. "I'm only good at opening pickle jars and potato chips."
"See, he's not qualified." Syrus said. "And neither am I, so why don't we just let it be?"
Jaden looked at the coffin for a few moments then started walking towards it.
He then pushed the heavy lid, slowly sliding it across until it fell on the other side with a loud thump. Inside they found a shriveled, dried up corpse. "A mummy… guess you won't be turning into a vampire yet. Hey, wait a sec… guys, bring your flashlights over here," he motioned to Syrus and Chumley.
"Why? What's wrong?" Syrus squeaked, holding on to Chumley in fright.
"This mummy looks… oddly familiar." The scared Slifers tentatively approached and passed Jaden a flashlight. He shined it into the coffin, allowing them to see that the mummy had a familiar black hairdo, glasses, and was dressed in a white lab coat and tie.
BANNER
"It is him..." Jaden stepped back a foot or so. "...Professor..."
"Wadda you mean?" Syrus asked, worried.
Jaden turned to his friend with a grim expression. "This is… or was… Professor Banner."
"That's impossible." Chumley said as they looked into the coffin. "He couldn't have mummified this fast. I can't even make beef jerky in the amount of time he's been missing."
"So… what? Is it a fake?"
"Of course," Syrus piped up. "It's a fake. Probably made out of wax or something."
"Wrong!" A grave voice spoke up as lights turned on, illuminating the room.
The boys all let out startled cries and turned around.
"That is the body of the one you know as Professor Banner." The mysterious figure who'd defeated their fellow key-keepers stepped forward. "Welcome, children," he said, giving them a mocking bow. "I am the last Shadow Rider."
"That's the one!" Ojama Yellow exclaimed, jumping out of his card. "He's the duelist who took down Chazz. And he's really good. But you gotta beat him to get Chazz back. You just gotta!"
"To get any of your friends back, you will have to beat me, Amnael."
"You're Amnael?" Jaden asked, surprised. "As in, the Mark of Amnael, Amnael?"
"That's right. And I have your friends right here." Amnael reached into his robe and pulled out his strange tome. "And if you cannot defeat me, you will be joining them. All of you."
"But what about Professor Banner? How do we get him back? Or is it too late?"
"It was always too late for him. It's best if you forget the one you knew as Banner. He is… no more."
"Wadda do you mean, no more!?" Jaden angrily demanded. "What is this? I wanna know just what you've done to Professor Banner!"
"To understand everything, you, both of you… must do just one thing. You must duel and defeat me. Only by working together will the truth be revealed. Only then will this tome and the secrets it holds be unlocked. Will you accept this challenge? Will you face me?"
Chumley shook his head at this. "Nope. No way."
"Uh, Chum?" Syrus piped up. "I think he means Jaden."
Syrus and Chumley looked at the mummy behind them and quickly moved towards the entrance they'd come through.
Amnael put away his tome and pulled back his hood, revealing a head of stark white hair. "Prepare yourself."
"Get your game on! Cuz we're getting our friends back, no matter what it takes, Amnael!"
Jaden: 4000 LP
Amnael: 4000 LP
"The first move is mine, Jaden, so I draw! And I play the continuous spell Chaos Distill. While this card is face-up on my field, any card that would be sent to my graveyard is banished instead," Amnael explained, Jaden wondering what he was up to. "And now I play the spell Steel Lamp. This card can only be played while Chaos Distill is on my field, and because it is, I may summon Alchemy Beast – Salamandra the Steel." Amnael explained as a metallic dragon appeared on his field.
Alchemy Beast – Salamandra the Steel: 500/500
"You see, Alchemy Beasts cannot be normal summoned, but in return, they can attack you directly, which is bad for you because I also play the spells Bronze Scale and Lead Compass, meaning I can now summon Leon the Lead and Ouroboros the Bronze!" He continued.
Leon the Lead: 500/500
Ouroboros the Bronze: 500/500
Amnael then placed a single card face-down and ended his turn. 
"He summoned three monsters in the very first turn?" Jaden marveled. 
"The standard modes of thought about dueling mean nothing when faced with my alchemy." Amnael responded. 
"My move. I summon Elemental Hero Bubbleman in attack mode!" Jaden shouted.
Elemental Hero Bubbleman: 800/1200
"And now I play the equip spell Bubble Blaster, which will give Bubbleman 800 more attack points!"
"Now Bubbleman, attack Salamandra with Bombarding Bubble Barrage!" Jaden ordered before Bubbleman launched a blast from his cannon at Amnael's monster. "Such a simple attack will not work against me. I play the continuous trap Elemental Absorber! By banishing a monster from my hand, all attacks from your monsters that have the same attribute as the one I banish are canceled," Amnael explained.
"It does what?!" Jaden exclaimed as a floating device with four metal spikes appeared on Amnael's field. 
"So by banishing my water attribute Aqua Spirit, your Bubbleman can no longer attack." Amnael informed as the last card in his hand vanished in a flash of light. One of the spikes on Elemental Absorber turned blue, a wall of water appearing in front of Salamandra, blocking Bubbleman's attack.
"I end my turn." Jaden concluded. 
"Very well, I draw. And now my Alchemy Beasts, attack Jaden directly!" Amnael ordered as Salamandra shot a jet of flames at Jaden while Leon fired a volley of lead shards from its mane and Ouroboros fired an energy blast from its mouth.
Amnael: 4000
Jaden: 2500
"Oh man, Jaden just got clobbered." Syrus noted, but Chumley pointed out that while he had fewer life points, he had an advantage since Amnael was down to one card in his hand. "Is that what you think? As I told you, my alchemy turns everything you think you know on its head," Amnael said before placing the card in his hand into his spell and trap zone.
"I play the spell Black Process – Negledo! Since there are no other cards in my hand and Chaos Distill is on my field, I may banish all my Alchemy Beasts in order to draw two cards for each one I banish," he explained before his monsters erupted in flames and were destroyed. 
"You're getting rid of your own monsters?" Jaden questioned.
"That is the way of the alchemist: destruction and rebirth. However, I can assure you that if you are destroyed here, there will be no rebirth for you. Now, since I banished three Alchemy Beasts, I may draw six cards. Next, I activate the spells Tin Spell Circle, Mercury Hourglass, and Silver Key! With them, I can summon Aretos the Tin, Ekenas the Mercury, and Moonface the Silver!" Amnael declared.
Aretos the Tin: 500/500
Ekenas the Mercury: 500/500
Moonface the Silver: 500/500
Amnael then ended his turn.
"Alright, I draw! And I summon Elemental Hero Clayman in attack mode!" Jaden shouted.
Elemental Hero Clayman: 800/2000
"And now I play the equip spell Mud Max! This card gives Clayman an extra 300 attack points." He explained as a dune buggy appeared on the field, Clayman stepping into it.
"Now Clayman, attack Aretos!" Jaden ordered before Clayman revved the vehicle's engine and drove towards his target. "Not so fast, I activate the effect of Elemental Absorber! By banishing the earth attribute Rock Spirit from my hand, your Clayman's attack is canceled!" Amnael said as giant stones sprung up in front of Clayman, stopping him in his tracks.
Jaden was frustrated he had been stopped again and ended his turn. 
"I warned you Jaden. To be triumphant, you will need to use your cards in a way that you have never used them before. I draw! And I play the spell White Process – Albedo! Since I control Chaos Distill, I can summon Golden Homunculus from my deck." Amnael explained.
Golden Homunculus: 1500/1500
"You see Jaden, this monster's attack and defense points are equal to the number of my banished cards times 300."
"It's over Jaden. And I was expecting so much more from you. Go my Alchemy Beasts, attack him directly!" Amnael ordered as Aretos sent a powerful gust of wind at Jaden while Ekenas launched a stream of water and Moonface fired crescent shaped beams of energy.
Jaden: 1000
"Now Golden Homunculus, attack Clayman with Stone Shard Storm!" he ordered as his monster fired a barrage of sharp stones at Clayman, setting off an explosion. "It's over," Amnael said, but Jaden called out, saying the duel wasn't finished yet. The dust cleared, revealing that Jaden was unharmed, but Clayman's Mud Max was gone.
Amnael asked how he survived the attack, and Jaden explained it was because of Mud Max. "When you attack Clayman while this card is equipped to him, I can destroy this card to negate your attack, and that's not all, because I can also summon a level four or lower Elemental Hero from hand, like my Elemental Hero Avian." Jaden said as his winged hero took to the field.
Elemental Hero Avian: 1000/1000
"Impressive. I end my turn." Amnael concluded before Jaden started his turn and summoned his Burstinatrix in attack mode.
Elemental Hero Burstinatrix: 1200/800
"Now Avian, attack Aretos with Quill Cascade!" Jaden ordered as Avian flapped his wings and sent a volley of feathers at Aretos. "I once again activate the effect of Elemental Absorber! By banishing Garuda the Wind Spirit from my hand, your Avian can't attack. And since another card has been banished, Golden Homunculus gains 300 more attack points," Amnael pointed out as a gust of wind blocked Avian's attack.
"I'm not done yet. Burstinatrix, attack with Burstfire!" Jaden declared as Burstinatrix launched a fireball at Aretos. "Not good enough Jaden. I activate Elemental Absorber's effect, banishing Spirit of Flames from my hand." Amnael informed as a wall of flames appeared, stopping Burstinatrix's attack.
"If my attacks can't get through, then I'll do something else. I play the spell Burst Return. Since Burstinatrix is on my field, every other Elemental Hero on the field goes back to their owner's hand," Jaden explained as Avian, Bubbleman, and Clayman went back to his hand. 
"Next, play the spell Burst Impact! When Burstinatrix is on my field, this spell destroys every monster but her, dealing their controllers 300 points of damage for each destroyed monster." He continued as Burstinatrix created a ball of white-hot fire in her hand before throwing it at Amnael's monsters, vaporizing all of them and cracking his mask right down the middle.
Amnael: 2800 
"Way to go Jaden!" Syrus celebrated before Pharoah ran into the room and up next to him. "Hey Pharoah, did you come to help cheer Jaden on? Well you can watch with us." Syrus said as he picked up the cat, but Pharoah scratched him in the face before running towards Amnael. 
"Don't!" Jaden shouted at Pharaoh to stay back as Amnael was dangerous, but he was surprised when Pharaoh began rubbing against Amnael's leg.
"I don't understand, Pharaoh is never that friendly with strangers." Chumley pointed out, Jaden saying that could only mean one thing. "That I am no stranger, to Pharaoh, or to you." Amnael said as he pulled his mask off, revealing his true identity to be none other than the missing Slifer headmaster.
"Professor Banner? But wait, if you're Banner, then who's that mummy?" Jaden asked. "That mummy is also me. My children, there is more going on here than you can possibly imagine, but the truth will be revealed soon enough," Banner assured.