We open to Ben and Y/n running for their lives from Dr. Vicktor and Ghostfreak. While they are fleeing, Vicktor tries to blast them with electricity, but Ghostfreak stops him.
Ghostfreak: "I need them alive for me to merge with one of them if I am to control the Omnitrix or the Ultimatrix."
Ghostfreak flies after the boys, but they are able to hide from him before he can see them.
Ghostfreak: "What's the matter, boys? Aren't you glad to see me? Haven't you learned by now that nothing can stop me?"
Ghostfreak phases through the wall the boys are hiding behind, forcing them to run.
Ben: "Nothing except..."
Ben activates the Omnitrix and transforms into Greymatter.
Greymatter: "Greymatter? Oh man. Gave me a break."
Dr. Vicktor jumps down from a catwalk above the boys and hits the ground with enough force to tear open the floor allowing Ben to escape. However, Y/n is now alone.
Ghostfreak: "All alone, Y/n."
Y/n: "Yeah, I dont think so."
Y/n activates the Ultimatrix and also transforms into Greymatter. He is able to escape beneath the floor, like Ben, before Ghostfreak of Vicktor are able to catch him.
Ghostfreak: "Find them! I cant merge with either of them in their alien forms. But it's only a matter of time before they turn human again."
Ghostfreak flies off in search of the boys, leaving Vicktor alone. After several minutes of searching, Vicktor is fed up with searching.
Vicktor: "Why are we chasing these little pests when the master plan is so close to becoming reality?"
Ghostfreak turns to Vicktor with a hiss and flies towards him. Ghostfreak phases into Vicktor, sending into a nearby wall. While inside Vicktor, Ghostfreak floats his body into the air and throws him into a pile of machinery, phasing out of his body just before impact.
Ghostfreak: "You fool. Those little pests could ruin everything we've planned. Do as I say, or you shall be the focus of my wrath."
Ghostfreak flies off to continue his search, however beneath the floor, the boys heard everything.
Greymatter(Ben): "Master plan? I dont like the sound of that."
Greymatter(Y/n): "Neither do I. We need to find a way to contact Grandpa and the girls."
Ben nods as the two microsized brainiacs descend further into the lab. The boys are eventually able to find a computer and use it to call Max and the girls.
Greymatter(Ben): "Earth to grandpa. Come in grandpa."
The boys are able to establish a video call with the others. On the screen they see that Max and the girls are in the cockpit of the space shuttle as it flies towards a space station in orbit. Max and the girls are also wearing level 10 hazmat suits.
Max: "We hear you Ben, is Y/n with you?"
Y/n pokes his head into the video.
Greymatter(Y/n): "I'm here."
Max: "Did you boys find anything out?"
Greymatter(Y/n): "Yeah, old bolt head is going to project a corodium beam from the space station to a transceiver in New Mexico."
Max: "Which will then spread it over the entire earth!"
Hope: "New Mexico? Like where we first took on the werewolf?"
Greymatter(Ben): "Right. That's why he stole that satellite dish. And probably alot of other equipment too."
Max: "A beam of corodium like that will mutate all human and animal like on earth."
Greymatter(Y/n): "I think that's just a side effect. With the sun blocked out, Ghostfreak would be at full power all the time."
Max/Gwen/Hope: "Ghostfreak?"
Greymatter(Ben): "Yeah. Dr. Monster somehow brought Ghostfreak back to life. He's behind all of it, the werewolf, Mr. Mummy, everything!"
Max then pulls out the corodium tracker.
Max: "Hang on a second boys. That's strange. According to this, the corodium inside this ship is moving."
Gwen: "How could it be moving? Unless..."
Max and the girls are suddenly entangled by the mummy's bandages.
Hope: "Its inside the mummy!"
They are then pulled from the cockpit by the mummy into the lower depths of the shuttle. Within the lab, Dr. Vicktor and Ghostfreak continue to search for the boys. While avoiding the terrible twosome, the boys get an idea to use the surrounding junk to build a miniature sun gun. Unfortunately, the boys time out just after completing it. The red glare from the Omnitrix timing out alerts Dr. Vicktor to their presence. The not-so-good doctor tears apart the metal flooring to reveal the boys.
Ben quickly pockets the tiny sun gun before Vicktor grabs the boys and throws them across the room, landing in front of Ghostfreak. However, Dr. Vicktor had accidentally made contact with the Omnitrix.
Ghostfreak: "Soon the earth will be mine."
Ben: "You want to be in the spotlight? How about this freak?"
Ben takes out the tiny sun gun and points it at Ghostfreak. Ghostfreak sees the tiny weapon and laughs. His laughter is stopped when Ben fires the gun, forcing a scream of pain from the alien specter as he flees.
Vicktor: "Master! You will pay for your insolence!"
Vicktor attacks the boys with his electricity, blowing a hole beneath them. The boys fall out of sight of Vicktor, whi smiles thinking he got rid of them. However, the boys silently climbed up behind Vicktor. The boys notice a large block of steel being suspended by a chain. Y/n pulls a nearby lever releasing the block. It hits Vicktor and sends him flying into the portal machine. A large jolt of electricity then begins to course through Vicktor, knocking him out.
Y/n: "Now we have to figure out how to get into space."
The boys notice and a rocket engine and share a smile. Ben transforms into Upgrade and merges with rocket. Ben creates a place for Y/n to sit and blasts off through the roof of the lab towards the space station. Unfortunately, they have a stowaway. Dr. Vicktor had recovered and grabbed onto Ben as he took off. But, Ben shot a laser form his eye onto Vicktor's face, stunning him.
Y/n: "Hey, Ben. I think the good doctor could use a hand."
Upgrade: "I agree."
Ben morphed a giant fist and punch Vicktor. Vicktor lost his grip on the rocket and fell, back towards earth. Ben was able to dock with the space station, and morphed into a space suit to protect Y/n from the vacuum of space while they made their way inside.
Once inside, the boys found that the mummy was attacking Max and the girls. Ben unmorphed from Y/n's body and forced the mummy into an airlock with his eye laser, sealing him in. It was at that moment Ben timed out. But, before the gang could celebrate their reunion, Ghostfreak reveals himself as he's preparing to fire the corodium beam.
Ben: "Ghostfreak!?"
Ghostfreak: "You're not the only one who can hitch a ride on a rocket."
The corodium beam had started a countdown, and they didnt have time to stop the firing. So Y/n did the only thing he could think of.
Y/n: "I wont let that beam hit that transceiver!"
Big Chill: "I dont have much time!"
Y/n phased through the hull of the space station towards the satellite that was firing the beam. Just as the beam fired, Y/n blocked the beam with his body.
Big Chill: "Aaaaaaaaahhhhhhh!!!!!"
The pain Y/n was feeling was unimaginable. The beam was slowly tearing his body apart. The edges of his wings had begun to burn, he could feel his bones beginning to crack and break, his skin began to crack and tear.
Big Chill: "Aaaahhhh... it hurts.. so much... but I.... will.... not.... move!"
Y/n didnt know for how long he was blocking the beam, the pain he was feeling made it impossible to tell. He could have been there for a minute or an hour, he didnt know. He just knew that eventually, the beam stopped. He slumped over and floated there in the dark void of space, barley clinging to consciousness.
Ben and the others had defeated Ghostfreak and stopped the beam. Using the space shuttle, they rescued Y/n. As soon as he was safely in the ship he fell unconscious and timed out. However, Ghostfreak decided to make one last appearance, attempting to steal Ben body again. However, they exposed Ghostfreak to the light of the sun and killed him, once and for all.
After returning to earth, Max and the kids rushed Y/n to a hospital, where he was taken to the emergency room. Max and the kids waited outside of the room for hours, going mad with worry over Y/n. Gwen and Hope were in tears, praying that he was going to be okay. Eventually, a doctor came out to talk to them.
Doctor: "Excuse me, are you the boy's grandfather?"
Max: "Yes, yes I am."
Doctor: "Well, I have some good news. Y/n was able to pull through and he'll live."
Max and the kids breathed a sigh of relief, however the doctor wasn't smiling.
Doctor: "There's also some bad news. Due to the boy's injuries, I'm afraid that he's fallen into a coma."
It was quiet in the hall. Not a sound. Max and the kids only stared, wide eyed, at the doctor. The doctor lead them into Y/n's room. On the hospital bed, Y/n was covered in bandages and stitches, and had an oxygen mask allowing him to breath. The only sound in the room was the steady beeping of the heart monitor.
The doctor left Max and the kids alone with Y/n. The girls went to either side of Y/n's bed and held his hands. At that moment the girls broke down. They couldnt hold the waterfall of tears. Behind them, Max and Ben were crying aswell.
After several hours, everyone had calmed down. It was now late at night and Max and the kids had fallen asleep in Y/n's room, unwilling to leave him.
After several days, Y/n still hadn't woken up. It was currently late at night and Max and the kids were asleep in Y/n's room again.
While they were asleep, a mysterious man entered the hospital and headed towards Y/n's room. He entered the room without waking anyone. The mysterious man walked to the side of Y/n's bed and looked down at him.
Mysterious Man: "You did a good job kid. Your medical report says you're likely to never wake up from this coma. Normally, that would be it. But, you're a remarkable young man. You've done remarkable things for this world, and you've paid a heavy price. And I believe you will continue to do remarkable things. You fell pretty hard, and the true strength of an individual is if they decide to get back up. But sometimes, people need a little help getting back up."
The man pulls out a syringe filled with a dark blue liquid, and injects it into Y/n's IV tube.
Mysterious Man: "Time to stand back up, kid."
The man leaves as quickly as he came. As he left, Y/n shifted in his bed.