@E3ora Molly's team will return to normal once this is all done. As for future evolutions and forms of Pokemon this story will mostly stick to gen 2 Pokemon like I said. Just the power of Unown pushed her team beyond the rules of space time, even giving Molly a futuristic Donphan.
"Just hold on Molly, we're almost there." Ash said, climbing the stairs to reach a terrace of sorts, with multiple towers heading further up. "More stairs, of course." Ash said.
"You are not welcome here." The Entei said jumping down from a tower to stop Ash's progress.
"You have some people that don't belong to you, and I intend to get them back!" Ash argued.
"They are happy and safe, but the same cannot be said for you!" The Entei argued, sending out a blast of flames.
"Wobbuffet!" Wobbuffet exclaimed, having come out of his Pokeball at an opportune moment, absorbing the fiery attack and sending the energy right back, destroying one of the crystal towers as Entei dodged it.
"Wobbuffet am I ever glad to see you suddenly." Ash said with relief.
"Wah!" Wobbuffet said, quite exhausted from the attack he took.
"Turn back now while you have a chance. Molly and her Mama are happy here." Entei declared as more crystals grew where the tower once was , with Entei leaping to another.
"Alright Pikachu, that's where we have to go. Mom and Molly are probably up there too." Ash said, returning Wobbuffet to his Pokeball.
"Pika!" Pikachu said, ready for the battle ahead.
Ash and Pikachu made their way right to the other tower as crystals covered the entrance.
"I don't think we'll be getting through it as easily this time." Ash admitted, seeing how quickly crystals were stopping them now. "I have an idea." Ash added, grabbing two Pokeballs. "Bulbasaur, Gligar, come on out!"
Bulbasaur was sent out at the top of the tower as Gligar came out next to Ash and Pikachu.
"Bulbasaur use Vine Whip and bring them down here!" Ash said, before grabbing both vines. "Gligar I'm going to need your help pushing us back up, slow and steady."
"Gli!" Gligar said in understanding, putting himself back to back with Ash as they worked to get him and Pikachu up the tower.
On television
"We're here up above the normally peacefully city of Greenfield where suddenly a large growth of crystals have been taking over the city from this spire where the mansion of famed archeologist Dr Spencer Hale is located." A news reporter said.
At the Pokemon center
"Everyone inside quick!" Lisa called out as crystals encroached on the building, locking them in.
"Come on Ash, we need you to save everyone." Professor Oak said.
Back on the tower
"One, two, one, two, one, twooooo!" Ash exclaimed, slipping before Gligar struck his tail into the crystals, stopping Ash from falling.
"Bulba!" Bulbasaur exclaimed.
"Are you alright Gligar?" Ash asked.
"Gli!" Gligar said reassuringly.
"Okay let's keep going." Ash said, picking back his pace up the tower.
In Molly's room
"What is this, it looks like someone is climbing the tower!" The news reporter said.
"Mama, look on the TV." Little Molly said. "He has Pokemon!"
Delia looked on the screen as Ash slipped momentarily. "Ash!" Delia said in shock.
"Did you say something Mama?" Little Molly asked.
"Mama?" Delia asked, remembering what was going on. "No, I just thought I saw something Molly."
The screen switched feeds as Entei came back in.
In Characific Valley
"It appears the person climbing the tower is alright, but what could be their goal here." The reporter said.
Charizard looked through the window into Liza's hut, seeing the screen with a familiar trainer on screen before taking off into the sky.
Back on the tower
"Great work you two." Ash said, returning his exhausted Gligar and Bulbasaur.
"I'll give you this, if nothing else, you are persistent." Entei said, returning once more.
"Yeah, we have that in common." Ash said. "Where's my mom and Molly?!"
"They are safe, the same cannot be said for the others in this castle however." Entei said, stomping the crystalline tower to shower crystal chrysalises containing Casey and the mansions staff.
"Let them go!" Ash cried out angrily.
"No, just like you they tried to take Molly from her family, and I will protect her!" Entei said, letting out a mighty roar.
"This isn't her family!" Ash said, standing his ground. "And maybe if I had been a better friend this wouldn't have happened."
"Molly has her Mama and me, her Papa, who are you to deny her of her truest wishes?!" Entei roared.
"I'm Ash Ketchum, and I have a dream of my own, to be a Pokemon Master!" Ash called out. "Pikachu use Thunderbolt!"
Pikachu sent out a bolt of electricity that Entei effortlessly leapt over before sending out a blast of fire, stopping the duo from moving forward.
"Pikachu use Thunder!" Ash called out.
Pikachu prepped electricity as the chrysalises of the captives went between them and Entei, stopping Pikachu from firing.
"Your connection to humanity makes you weak. You could join us and be happy." Entei said to Pikachu.
"Pi!" Pikachu said defiantly, standing next to Ash.
"Pikachu use Agility to get around them and hit Entei!" Ash called out.
Pikachu sped around the chrysalises, making his way behind Entei before striking the fire type with a juiced up punch.
"Insolent whelps!" Entei roared, knocking Pikachu back into Ash's arms. "I offer you a chance to turn around, and you refuse. I offer you a chance to join Molly's happiness and you refuse, when will you understand you are not wanted here!"
"You're wrong about that Entei." Ash said, standing back up. "Deep down Molly wants us here more than anything, and maybe right now she doesn't know that, but I know for a fact that if she's the one causing all this, we wouldn't be all the way up here if she didn't want us to be."
"No, but that can be easily changed." Entei said, unleashing a powerful blast of fire sending Ash flying off of the tower and mansion to the crystal precapace below.
"Ash!" Delia exclaimed, watching from a window.