The scene with Yellow, Lance, and Petrel in the HGSS chapter is making the fandom go crazy, so I thought I'd give my version.
Note: I'm using the Japanese names of the characters and attacks.
Wataru smirked as his opponent's last Dogars fell, leaving him with no more party members to fight with.
"Ready to give up, come clean, and stop this madness, Lambda?" Wataru smirked, his kairyu standing over the man like a towering colossus, awaiting the next order.
Lambda smirked. "You are certainly as strong as the rumors say, dragon tamer. But do you really think that you will stop Team Rocket? Once we have Arceus' power, we will rule the world, something you failed to do quite a while ago."
Wataru grimaced, remembering how he and the other members of the former Kanto Four Heavenly Kings almost eradicated the entire human race. Of course, they were stopped by a young girl from the Tokiwa Grove.
"This is different! I had a reason...and all you have is desire for bloodshed and power! Kairyu, destruction beam!"
The mighty dragon reared back and shot the yellow ray in the villain's direction, making a huge cloud of smoke appear. The smoke blocked Wataru's vision, making it hard to locate Lambda.
"Where'd you go, coward?!" Wataru yelled into the blackness.
Suddenly, a feminine giggle resounded in Wataru's ear. He stopped, pulling his cape in front of him to help him breathe.
"Dammit! Why'd I have to separate from Yanagi and Sakaki?! Laplace's chilling wind would really come in handy about now!" Wataru thought frantically.
Kairyu, whose beating wings helped clear the smoke, moved behind Wataru, hunched to strike. Wataru's eyes widened at the sight in front of him.
A young girl floated in front of him, supported in the air by a golbat. She looked no older than eighteen, and her long, blonde ponytail washed down her back like a waterfall. She wore a standard Rocket Executive uniform, without the hat.
"It's been a long time, Wataru. I trust you are well?" She said, smiling.
"No..." Wataru's eyes widened. "Yellow...you work for them?"
She giggled at the question, as if she was asked if she liked existing. "Of course. Did you actually think pokemon were worth treating with respect?"
Wataru's hand balled to a fist, and his head fell. "But, why?"
"Well," Yellow began. "I finally saw the truth. Pokemon are only useful for making money and world domination, and after obtaining the power of the Shin'o gods, we will achieve our goal." The emphasis on the word "will" was frightening.
"You've gone mad!" Wataru growled. "I will not allow this! Kairyu, destruction beam!"
Kairyu thrust its chest out as it released the attack from its mouth, resulting in another explosion and smoke cloud. Yellow dodged the attack deftly on her golbat, sending out two matadogars and a ratta.
"Certain-kill fang! Smog!" She commanded. The ratta charged and buried its fangs into kairyu's hide, and the smog prevented Wataru from helping him.
"Ptera! Blow the smog away!" Lance cried as he threw the hyper ball in the air, releasing him.
The dinosaur began to beat his wings, blowing the harmful gas away. Yellow wouldn't have any of that.
"Matadogas, lightning!" She cried as the two poison-types released hundreds of thousands of volts of electricity. It was a direct hit on Ptera, sending him to the ground with a crash.
"Dragon pulse!" Wataru cried as kairyu flung the ratta off. The blue beam sent the ratta flying back towards its master, knocking it out.
"Sludge bomb, smokescreen!" Yellow cried. Smoke erupted into the air as a large ball of dirty sludge flew towards Wataru, landing a semi-direct hit. The sludge's stench was vomit-inducing, and it clung to the cloth of Wataru's ornate clothes.
"What's the matter, Wataru? Are we going to have the same result as last time?" Yellow chided as she landed, the golbat flying away.
"No! You will lose! Destruction Beam!" Wataru commanded again. The beam struck the two matadogars, effectively knocking them out as they fell to their master's feet.
Yellow began to clap slowly as she walked towards Wataru, smiling all the way. "Bravo! You win!"
Wataru backed away, fearing a trap. "Yellow, I can't believe a good person like you would become a part of this evil organization. What about your friends?"
Yellow put her finger to chin, as if she was in deep contemplation. "Most of them are just living their lives, and I don't keep contact with them. Not like I care, anyway. On the topic of joining, don't you think it's obvious that when Sakaki came to my assistance on the island, the deal was already sealed? Chew on that for a while."
"Please reconsider. Stop helping them." Wataru commanded as he tensed, ready to give kairyu another command.
"What makes you think you can boss me around?" Yellow giggled, putting her arms behind her back.
Without warning, Wataru felt a sharp pain on his side. He turned, and to his horror, saw Yellow's golbat clamped down on his rib cage, using excessive poison fang.
He smacked the thing off of him, falling to his knees in pain. The poison was beginning to seep in, stealing his consciousness away like a thief in the night.
"Goodnight, Wataru, dear." Yellow said, laughing maniacally as his eyelids became heavy.
Waking several hours later, Wataru looked to see his shirt and cape removed, his pokemon in their balls on the ground next to him, and someone in a wheelchair facing away from him.
"Ah, you have awoke. How are you feeling?" The man turned, driving his wheelchair towards him.
"Yanagi, thank you. Where...is she?" Wataru asked, pain in his voice.
"Save your energy, I'll explain." He turned his chair, looking away in the distance. "The one you thought was Yellow was not all she seemed. Let's just say...Lambda is a master of disguise."
Wataru's eyes widened at the realization that he had been had. Anger and relief filled his heart, but mostly anger.
"That bastard...playing to my weaknesses..." Wataru grumbled through gritted teeth. "Did you catch him?"
Yanagi shook his head. "No. Sakaki went on ahead, but we will catch up. Apparently, some young children are fighting the rockets right now. The very same children that apprehended me many years ago."
Wataru couldn't help but laugh at his old friend's sentimentality, but he knew the direness of the situation. "The dexholders?"
Yanagi nodded slowly. "Just three. They're in way over their head. Sakaki's son is involved, so we need to get help him."
"I never knew he had a son." Wataru said to himself. He stood up, feeling very little pain. "Let's go."
Yanagi nodded as he called out Wataru's ptera, and Wataru mounted kairyu.
"I knew that couldn't have been you, Yellow. I fell in love with the kind-hearted healer, not a rocket executive."
With that thought, they flew off, ready to destroy that blasted organization forever.