I thought this was a great chapter. I can't wait for the next chapter. Here are the errors I saw.
It was a clear day in Viridian forest, and Kyle was sitting in a large clearing, his feet dangled lazily beside a shallow river. The small waves embraced the banks before being wrenched aside and pulled downwards towards Pewter City's water dam.
"No I won-" Cindy began before she her legs lost their grip and she fell, face first towards the ground.
"Poliwag, use bubble," Kyle said through a heavy sigh as from beneath the water emerged a small round Pokemon which Kyle had received from Giovanni. The tadpole pokemon shot a bubble (which was around 5 times his size) at Cindy, who hit into it and bounced, landing with a loud thump on the ground.
"You know something; you shouldn't laugh, for all you know I could be seriously injured from this," Cindy began as she stopped rubbing her head. She then turned to Kyle who was now pale; his pupils were so small you could have thought he had none.
"What?" Cindy said as she heard a cold and constant buzzing. She turned to see an uncountable amount of Beedrills behind her as she opened her mouth and let out a deafening scream.
No less than 30 seconds later, Kyle, Cindy, and Poliwag were running for their lives from a seemingly endless supply of Beedrill. No matter how hard they tried to escape they just couldn't shake them. They turned, they dove, and they moved to high ground, to low ground, they went through bushes and through water but Beedril don't give up in a chase.
Kyle turned on his heel, he was done with running. He reached for two Pokeball's on his belt and cried the name of his beasts that dwelled within, the flash of light signified their acknowledgement. Within seconds the Beedrill had formed a circle around Kyle, Poliwag, Pidgey, and Charmander, all of whom were fighting for their life.
"Charmander use ember now, Poliwag keep up that water gun, and Pidgey use wing attack on the one on the left!" Kyle cried as the forest was hypnotized by the flashes of light and the orchestra of destruction as the Beedrill continued to crash in useless heaps onto the ground.
The battle went on for what seemed like an eternity. Kyle, Charmander, Poliwag and Pidgey were all exhausted and the Beedrill where still coming in the hundreds. Kyle felt a chill go down his spine, as from behind him he heard a scream. He turned to see Charmander in the direct lines of fire from five Beedrill and there was no time to think, only time to react. Kyle hurtled forwards, jumping across Charmander, using his chest as a barrier from the malicious Pokemon.
It may have simply been his imagination but as Kyle fell to the ground, the thick 5cm needles from the Beedrill sticking out from all angles of his chest, he could have sworn he heard a voice. It, however seemed distant, and it was echoing inside the deep catacombs of him mind.
The voice died away and Kyle saw only a blinding light. Kyle's eyes were slowly adjusting to the bright light and through his clouded vision, he could make out a corridor. Kyle was moving, but he couldn't control what he was doing. He was a puppet on a string as his master guided him through the pale and lifeless corridor until he came to a dead end, or at least what he thought it was. From the pale, dead, wall emerged a door; the handle gave a light click as Kyle's hand automatically opened it.
The further Kyle ventured into the room the more confused he became. It reminded him of a very bland and pointless piece of modern art, but he kept moving forward until he was standing in the center, and then it happened.
Kyle heard an aching noise, as if the ground was going to give way, and then the center of the room began to move upwards. Higher than the ground, the small pillar which he was standing was going higher and higher, and the pool was no longer visible below him. Then it came to an abrupt halt and Kyle stood, alone, in the semi darkness. But if he listened as hard as possible he could hear heavy breathing. There was a bang as all around him people appeared, there were four of them in all. Kyle didn't recognize any of them, save one. Giovanni was standing opposite him, his hands behind his back as he opened his mouth and began to chant.
And to Kyle's utter confusion he found himself cry "Air," and then the room filled with blue, red, yellow and white light. In front of them there was a loud crash and before him, Kyle saw the silhouette of a Pokemon so powerful his inside burst. He keeled back and fell into the pool of oblivion that was the darkness below him
Kyle bolted upright, his hands were covered in blood as his eyes filled with tears. He was sitting on top of the mossy, forest floor. He looked left to see Charmander lying unconscious by his side, he tried to reach for him, but felt a pain like no other. He clutched at his chest and fell onto his back and stared upwards at the small glow of orange light that was barely visible through the large branches of the trees.
"Thank god," Cindy cried as she noticed Kyle was awake, before placing a cold flannel on his head and examining the wounds on his chest.
Kyle didn't have the energy to say anything, but if he could he would have asked how Charmander was and were Pidgey and Poliwag ok, but these thought where ones that would haunt him as he slipped back into nothingness, his mind racing with dark thought of the fate of his Pokemon.
The main thing that I see you do is that you run on your sentences with commas. Other than that, it was great. Good job!