@Thor94
Unfortunately the timing this time is when it's all getting past the point of needing a legendary, however as I've said this story isn't done, and there is more for Zekrom, plus the plan for the upcoming fight is a bit of a strange concept based on some canon material.
"Where, where am I?" Ash asked, rubbing his eyes, trying to look around, only seeing inky blackness. "Pikachu! Charizard! Are you out there?!"
"Pika!"
"Grawr!"
Their cries of battle echoed out through the area, but Ash could not see any sign of either of them.
"Well I'm not blind, and I don't think I'm dead." Ash said, looking down at his arm and pinching it. "But that still doesn't answer the question of where I am."
As Ash looked around, seeing a swirl of yellow and blue electricity opening to show a window nearby.
"I guess that's better than inky blackness." Ash admitted, floating towards the window.
"Alright Zekrom, since you don't want to come out, we'll try something a bit unique." Damon said, grabbing a crystal.
"Damon?!" Ash asked in shock. "I thought you gave this up! Wait, this lab, it's not destroyed yet, this is the past, are these your memories Zekrom, and what is that crystal?"
Ash watched as the crystal was pushed towards the window, absorbing into the view.
"With this crystal I should be able to force control of you with Burst power." Damon said, as the area began to glow, the window closing.
"Burst Power? What did Damon do to you?" Ash asked, trying to find the crystal. :And why are you showing me all of this."
Another window opened, showing the skies over Unova, a drawing feeling towards something, even Ash could feel the draw.
"Where are you taking me?" Ash asked, as the storm clouds cleared with an opening, showing himself and Pikachu on the docks.
"This is the day we first arrived in Unova, when you attacked Pikachu and me." Ash realized, before feeling Zekrom's feelings.
"You didn't attack us, you were trying to recharge." Ash said in shock. "And we attacked you in retaliation."
Ash looked away from the window.
"This whole time, you've been weak, low on energy, even back in your stone you haven't been able to fully recharge, thats why you haven't re emerged ever since we fought Kyurem. It's because of that Burst Energy isn't it?" Ash asked.
Ash could feel as if Zekrom was telling him yes about all of that.
"Okay, then this time, we fight together, and I'll take the Burst out with me." Ash said. "That's where I am, aren't I, this is the Dark Stone."
As if to show the truth, the area illuminated, showing Pikachu and Charizard fighting the still fused Kyurem that seemed to be out of control.
"Zekrom, please release Ash, we need him." N said, looking at the dark stone.
"Take me to the Burst Crystal." Ash said, as the large crystal floated towards him. "Alright, let's do this!" Ash exclaimed, electricity flowing over his hands.
Outside
"Zekrom? Is that you? Where is Ash?!" N asked, as a black being emerged from the stone.
"We're both here." Ash said, turning his head to show him in a Zekrom like armor.
"What is that?" N asked in shock.
"We call it Burst Heart." Ash said. "Charizard let's go!"
"Pika!" Pikachu exclaimed hopping onto Ash's shoulder as he took off in flight alongside Charizard.
"Lightning Perfect Wave!" Ash called out, firing a ball of electricity from his clawed hands as Charizard and Pikachu combined their attacks alongside it, blasting into Kyurem.
"That Burst Mode! Damon said it was impossible!" Ghetsis exclaimed. "Kyurem use Ice Burn!"
"Charizard use Flamethrower!" Ash called out, his voice echoing with a roar as he flew into the air. "I have to stop that ship from crashing, Zekrom full speed!"
Ash and Zekrom rushed forward, towards the ship, grabbing the front end of it, seeing his friends inside.
"Ash?!" Rosa, Elliot, and Hugh said in astonishment.
"It's a long story, but I'm going to land this!" Ash yelled, digging his claws into the metal as blue lines of electricity glowed across his body and Zekrom's tail.
"Mello!" Melloetta said, joining him outside, pushing the ship to safety.
"Everyone brace for impact!" Ash called out, pushing back against the ship as it came for a crash landing.
"Mel Mel!" Meloetta cheered.
"Stay with them! I need to get back!" Ash said, as he heard Charizard's cry in the distance.
"Now Kyurem use Glaciate! Hydreigon use Crunch!" Ghetsis commanded.
"Get away from him!" Ash exclaimed, slamming into Kyurem, giving Charizard the opening to dodge Hydreigon's attack.
"Are you sure Zekrom?" Ash asked, hearing the dragon in his head.
"Kyurem kill that insolent bug!" Ghetsis commanded.
"Not today. LIGHTNING SPARK!" Ash yelled, an explosion of electricity engulfing him and Kyurem.
As the blinding light of the explosion cleared, Ash stood back up, now shed from his fused form with Zekrom, holding the three stones in his arms.
"It's over Ghetsis, you have no control, no dragons, and no king." Ash said, staggering slightly.
"It is not over! I am still the superior trainer and I will beat you once more and take all three dragons once again! Then I will freeze all of Unova and reign as King as the only remaining trainer to control these beasts!" Ghetsis yelled, causing the arena to come to a standstill.
"I! Am! Never! Running! Like! That! Again!" Elliot said, having gotten the cameras back on just in time for Ghetsis to reveal his true plans.
"N, hold Reshiram." Ash said, handing the other trainer the Light Stone. "I trust you to keep her safe. Charizard, Pikachu, ready for our champion match?!"
"Pika!"
"Grawrh!"
"Very well if you wish to play that way so be it, I don't need an army to defeat you! Hydreigon use Surf!"
"Charizard use Seismic Toss!"
Authors Notes
Yes, with all the delays of the league alone, I came up with a slightly better reason as to why Zekrom struggled forming and staying, rather than because it was tired of losing. As for the Burst Mode, that is an actual thing from the Japan only generation 5 manga titled Re-Burst, where the main character's ace is none other than Zekrom, so no I didn't come up with the anthropomorphic fusion of human and Zekrom on my own. Even the attacks Ash-Zekrom used were from the manga.
Next time, the final fight against Ghetsis, final chance to guess those mysterious four other Pokemon Ash brought along. And again, this is not even close to the finale of the story, there are plenty more characters, stories and locations to explore, and more screen time for Zekrom, probably.