ALONE AGAIN

Chapter 1: A new start
Danny lay on the floor of his cell, quietly crying. Even after a year with the GIW, the memory of his families deaths was still fresh. Everything reminded him of them. He had flashbacks constantly, triggered by seemingly random things. The pain was so bad, it was like an open wound. And thanks to the anklet keeping his healing powers from working, he knew what that felt like.
'I miss them too. I promise Danny, I'll never turn into him.' Phantoms
voice said quietly in his head. Danny sighed. 'Thanks Phantom.'
The door opened and light flooded the room, outlining the tall agents sent to fetch him. Danny felt dread swell up inside him. What horrors would he be subjected to today?
The agents entered and yanked him roughly to his feet.
"Hey ghost kid,"one hissed,"we're doing something new today." He grabbed Danny's chin and forced his face upward. "Soon, you won't need to worry about anything at all."
Danny's eyes widened. He couldn't mean-he was far too valuable. And yet...
'He's just trying to scare you.' Phantom insisted. Danny wished he could believe him.
The agents dragged him toward the all too familiar lab. Despite his weakness, Danny struggled. The agent to Danny's left grunted. "He's a rowdy little guy, isn't he?" The other agent growled. "Unfortunately, yes."
Despite all his struggles, he was soon strapped to the examination table he had come to know so well. He squeezed his eyes shut. Could this be it? After all he'd been through, would this be the day it all ended?
"Ah, hello Daniel. How lovely to see you." Danny opened his eyes to see Dr. Kert Azy. Danny just called him Krazy.
"Still not talking? Oh well, I suppose it is hard to talk if your living off a cup of water a day." Danny bristled, and chocked,"Just get on with it." He winced. His voice sounded worse than Tucker's singing. Tucker...
Krazy feigned surprise. "My subject lives! Although you won't soon." He saw Danny's expression and laughed. "Oh, I see you've figured it out."
"But-but you need me!" Danny stuttered, unable to disguise the fear in his voice. Krazy laughed,"We need some tissue samples, a few pints of your blood, and your ghost half. But we don't need you, per say." Danny's eyes narrowed, "What do you want with Phantom?"
"You care about it, how sweet." Krazy smiled, walking to the other side of the room. "You see, even though we're barely giving you any food, we're currently suffering major budget cuts. So we came up with a simple solution." He came back with a tray of painful looking tools. "If we can successfully separate you and it, we won't need to worry about feeding you anymore." Danny tried to squirm away from him, but the restraints held him fast.
Krazy took a pair of scissors and snipped off his once white T-shirt. "It's nothing personal. We just don't want to worry about your needs anymore." He tore through the flimsy stitches keeping Danny's Y cut closed, and Danny clamped his mouth shut, refusing to let this sick man know how much it hurt.
"It's a fairly simple process. I just take this knife," he held up a short scalpel,"and stab your ghost core in just the right place..." He stabbed down.
The pain surged through him like so many volts of electricity, worse than any pain he had ever felt in his entire life. It was worse than when Vlad tried to force him to morph, worse than when the GIW tested his tolerance to heat, worse than when he became half ghost.
Krazy flipped a switch, and volts of electricity really did course through him. Danny could hold his cries of pain back no longer, and screamed loudly. Krazy smiled a cruel smile, watching him suffer for a moment, then took a long, glowing hook from the tray. With a triumphant smirk and no small amount of flare, he jammed the hook down Danny's throat. Danny squirmed, but Krazy kept moving the hook around. After a minute, he found what he was looking for and yanked it out.
Phantom came off the hook and hit the floor with a meaty smack. He looked awful. He was covered in blood and ectoplasm, and it made his hair stick out at strange angles. He was bleeding from all sorts of open wounds, all of them matching Danny's perfectly, including the Y-cut. Despite all this, he managed to lift his head and croak, "Danny?" His eyes widened when he saw the still form. "DANNY!"

Phantom woke with a start, his core thrumming. He thought back on his dream and immediately curled into a ball, tears running down his face. It had been four months since they had killed him, four months since they'd ripped him from his human half and watched as Danny died. He could remember when he had merged with Danny. He had been a lonely ghost with no reason to exist, floating around in a depressed state that would have made Spectra forever young. Then he had seen him in the half formed portal, screaming in pain. He had flown in, trying to do something, anything to help the poor teen in the portal.
He hadn't expected to become half human that day. He hadn't expected to wake up with no control of his body, to be a passenger as Danny used his powers to fight the evil ghosts that came through the newly formed portal. But that's what happened, and Phantom wouldn't have had it any other way. They had formed a bond closer than brothers, with Phantom helping Danny with personal issues and Danny using his powers for the greater good. They had been inseparable, one being.
Until the GIW killed him.
Phantom remembered his screams, his glassy eyes as he slumped down, dead. After Danny died, everything became blurred. He had barely registered that four months had gone by. He vaguely remembered more experiments, more pain, but until the escape there wasn't much.
The escape. Thinking of it, Phantom had to smile. It had been ingenious. Amorpho had snuck in and pretended to escape as him. While all the guards were distracted, Ember, Skulker, and Technes broke in and found the real him. After everyone got outside, Wulf had opened a portal to the ghost zone and they were home free. Phantom was currently staying with Clockwork.
Phantom sat up and walked across the room. He fumbled around until he found what he wanted-his sketchpad. Flopping down on his bed, he wiped away his tears and began to draw. The drawing pad was a gift from Ghost Writer, and it was helping Phantom with his grief. Whenever he felt like his life-afterlife wasn't worth it, or he was crying himself silly, he could find peace with his paper and pencils. Spectra told him everyone dealt with loss differently. Some people pulled into themselves, some lashed out at anyone they could blame, some people worked harder than ever before. He drew. He drew memories, friends, objects of meaning, the way things could have gone differently. It was how he dealt with things. He decided to draw Wulf and Danny. He was just adding the finishing touches when he glanced at the clock. His eyes widened. It was that close?
He packed his satchel with his sketchbook and pencils, the I-pod and headphones Ember had given him, the Box ghosts box charm, the Lunch ladies goodie bag, and the Fenton thermos.
He walked downstairs, stopping at the bathroom to grab his toothbrush and pain medicine. Even though his power inhibiting anklet had been removed, Clockwork told him it could be as long as a year before his healing powers fully returned.
He paused in front of the mirror, examining himself. He had changed his getup since arriving at Clockworks. He wore dark jeans and a gray long sleeve, with white sneakers. He also wore a black hoodie, which he kept unzipped most of the time, and his satchel was gray with black accents. His face hadn't had many changes, except for a pale scar above his left eye. His hair was still white as snow, and he kept it the same messy style Danny had liked. The neon of his eyes had faded so they only glowed when he was angry. His right leg was twisted outward ever so slightly, but the limp was so subtle you didn't notice unless you looked very closely. If he walked down the street in Amity park, he couldn't say if people would know him or not.
He shook himself from his musings. He wouldn't need to worry about being recognized where he was going.
He hurried down the stairs, where he found baby Clockwork calmly winding his staff. "I was beginning to think you had forgotten."
Phantom rolled his eyes,"Yeah right. You knew what I was doing up there the whole time."
The keeper of time smirked, showing his buck teeth."I also know that you're ready to go." A few days previously, Danny had asked to crossover to a parallel dimension. He figured he could start a new life, away from the his past and his pain. "Yeah, I'm ready."
Clockwork, now middle aged, waved his staff and a rainbow colored portal swirled into existence. "This will take you to the dimension I have chosen for you. Remember to only take your pain medicine after you eat. It would also be wise if you avoided direct blows to the chest until you are fully healed." Phantom just nodded, not telling Clockwork that he was acting like a worried parent, and stepped forward. Just before he went through it, he turned to the Time Lord. "Thanks for everything, Clockwork." Then he stepped through the portal and was gone.
Clockwork watched for a moment, then closed the portal with another wave of his staff. He reflected upon Phantoms decision. He had been reluctant at first to allow him to leave, but after looking into his possible futures, he had agreed that it would be best for him. His futures in this dimension had not been pleasant.
Clockwork floated over to his time screens, shifting into an old man as he went. With a wave of his staff, he opened a screen to Phantoms new home. He wondered which route time would take.

-Line break-

When Phantom came out of the portal, he didn't expect to step on someone's face.
He and said person fell into a heap on the floor. A hand reached for him, and he automatically lashed out with his fist, sending the person flying across the room and through a wall. He stood up and looked at the new hole in the wall. "Uh." His super hearing picked up voices to his left, and he whipped around.
Facing him was the strangest group of beings he had ever seen, and that was saying something. A green man with a blue cape, a black man glowing green, and a hot woman in an American themed swimsuit were floating in the air. On the ground below them was a woman with a mace in her hand and wings on her back, a man in a black suit and cape with a fancy utility belt, and a man in a red jumpsuit with yellow lightning bolts on his head.
"Where did this guy come from?" The man with the lightning bolts said.
"Who cares? He just knocked Superman through a wall." The girl in the swimsuit lunged forward.
"Wait-" Phantom started, but her fist slammed into his chest and he went flying.
He flew straight and true, slamming through a wall before slumping down, seeing stars. He felt something on his chest, and when he pulled his hand off, it was green and sticky. It would also be wise if you avoided direct blows to the chest until you fully recover. Oops.
He looked up to see the group of people staring at him, or more specifically, the ectoplasm leaking from his chest. He got up and flew as fast as he could, trying to get away. He didn't know who they were, but he wasn't strong enough for a serious fight. He flew faster than he had in over a year-
And promptly ran into a brick wall. He dropped several feet before regaining his senses and stabilizing. When he looked up, he realized what he had run into wasn't a brick wall; it was a man in a blue and red suit, with a large S on his chest. Oh, he thought, this must be Superman.
"Superman" tried to grab him, but he ducked out of the way. Thinking quickly, Phantom grabbed his cape and spun him around, throwing him into the ground. Then he flew off, ignoring the others calls to stop. He phased into a nearby warehouse and slumped against the wall. He looked down and was shocked by the amount of ectoplasm on his shirt. He was bleeding a lot worse than he had originally thought. In fact, he was feeling a little faint...
Phantom slumped to the floor, his last thought being of how crappy this dimension was.

-Line break-

Green Lantern was, in a word, pissed. He and Batman had just gotten back from an extremely complicated time traveling mission, and he had been looking forward to some relaxation. But then, just when he was getting things straight in his head, J'onn got a call requesting-no, demanding the original seven members of the Justice league to meet them at the warehouse docks to pick up a "special package". Even though he had thought it was a prank, the others had insisted on going. And guess what? A portal appeared, Superman got thrown through a wall, Diana punched some random kid through a wall, that kid started bleeding some sort of green liquid, and Superman got smashed into the street.
"Terrific! Just great!" He yelled, his anger causing his voice to rise. He rounded on Diana,"Did you need to punch him?"
"I didn't know he had been previously injured." Wonder Woman tried to defend, but was cut off by Batman.
"This is no time to point fingers. We need to find him. J'onn, could you do a telepathic sweep?"
J'onn shook his head. "While he was here, I attempted to enter his mind, but could not."
"Wait," Flash said,"His mental shields were strong enough to keep J'onn out? Who could do that?"
Superman stood up, brushing himself off. "Well, whoever he is, he couldn't have gone far. Lets spread out and find him."
Green Lantern flew off, still steaming slightly. He entered a warehouse, using his ring to light his way. "Kid? Are you there?" He turned a corner, still searching. "I promise not to hurt you-" he saw a slumped form on the floor. Flying over, he saw the boy had lost consciousness. He picked him up as gently as he could. He turned on his com link, "Guys, I got him."

-Line break-

As J'onn exited the medical wing, he was mobbed by curious heroes.
"Who was that J'onn?"
"Where did he come from?"
"Is he going to be okay?"
"Was he the special package?"
"QUIET!" Silence instantly reigned supreme. No one wanted to tic off Martian Manhunter.
"All your questions will be answered in due time. Until then, return to your normal duties." The heroes slowly dispersed, muttering once they thought that J'onn couldn't hear. The Martian called,"Kara?" Supergirl turned. J'onn motioned her over. "I need you to watch our guest." Supergirl groaned and he added,"Do it or you're The Questions personal assistant for a month." Kara gulped and nodded.
J'onn flew up and phased through the ceiling into the conference room, coming up behind Shayera.
"I've treated him as best I can-" Shayera visibly jumped, turning with her mace raised. She stopped it two inches from J'onns face. She slowly lowered it,"Someday somebodies going to knock your head off."
J'onn stood, unblinking. "As I was saying, I've done my best to treat him. But I still have no idea who, or what, he is."
The others looked at each other. Finally Batman spoke, "Maybe we'll find some answers in this." He held up a gray and black satchel. He dumped its contents onto the table.
Everyone stared at the strange assortment of items before them. Flash picked up what looked like a fancy soup thermos. He opened it,"Hey, there isn't any soup in here!" Batman glared and he quickly added,"I mean, why have a soup thermos when there's no soup in it?"
Diana picked up a charm. It resembled a closed cardboard box. "I wonder what this is for." She asked, feeling it with her fingers.
Shayera shrugged, picking up a small leather bag. "Who knows? Maybe-" She stopped as she tipped the bag upside down and a dozen peanut butter cookies fell out. Her mouth dropped open, and Flash started to salivate. The combined glares of Batman and J'onn were all that kept him from stuffing his face.
After a minute, Green Lantern said,"Well, our kids got some weird stuff." He picked up an I-pod and scrolled through the playlist,"He does have good taste in music."
Batman picked up a small orange bottle. "Looks like he takes pain medicine." He studied it for a moment,"Doesn't say where he got it."
"Maybe this can give us some answers." Shayera held up a reddish brown book.
If anyone had entered the room at that moment, they would have a hard time not laughing at how earths greatest heroes crowded around Shayera to get a peek at the book. Only Batman managed to look dignified.
Shayera opened the book, and tucked between the first page and the cover was a handwritten note. Diana took it out and read it aloud.

Dear Phantom,
I hope you will not disregard this message as mere words, but understand it for what it is-a plea for forgiveness. I am sorry to be so uptight, especially concerning my books. I can not pretend I understand what your through, since I never had any close relatives in life. Clockwork has told me that you enjoy drawing, so please accept this sketchpad as a plea for forgiveness regarding what happened at Christmas. Hopefully it will be able to help you with your grief as well.
(Hopefully) Your friend,
Ghostwriter
P.S. If you're wondering why I'm not rhyming, Dora translated for me.

The heroes looked at each other, confused. Who were Clockwork and Ghostwriter?
Green Lantern spoke,"Well, at least our mystery boy has a name."
"But who's Ghostwriter? And what did this "Phantom" go through?" Superman asked.
"And what did he mean by "translated"?" J'onn persisted.
Batman shook his head. "I guess we just keep looking."
Everyone crowded around again as Shayera turned the page.
The first drawing depicted the teen in a black and white hazmat suit hanging by his neck from a tree. His eyes were open to reveal empty black sockets, and under the tree was a single word-Why?
Shayeras hands tightened on the book as they stared at the picture. With a shaky breath, she turned the page.
The next showed Phantom standing on the edge of a building, with one foot hanging over the edge. Above his head was the word-Goodbye.
Shayera took a deep breath, gently setting the book on the table. Green Lantern looked at her with concern. "Are you alright?" She nodded,"I just...need a second."
"I can take it if you want." He offered.
Shayera shook her head. "I can handle it." She picked up the book again, making sure her hands didn't shake.
The next several minutes weren't much better. All of the pictures were tragic and violent, with many being suicidal. Shayera had to stop every couple pictures, and no one could really blame her.
Finally Flash said,"Look, I don't know about you guys, but all this is doing is depressing me. Maybe we should just ask him who he is."
"Wait." Batman pointed at the book. "It's divided into sections."
Shayera looked more closely. "Yeah. Let's see, we're in 'Before therapy'."
"Maybe 'After therapy' will be less suicidal." Superman suggested. With a nod, Shayera turned to the section.
The first picture was of a person. At least, sort of like a person. It was a young man with a scar over his left eye. His chest was a pane of glass, showing mechanics similar to a grandfather clock. He wore a purple cloak with a gear clasp, with black gloves and a belt with stopwatches on them. In his hand was a staff with a clock perched on the top, and he didn't appear to have legs. He had a smirk on his face, a look that said 'I know something you don't. ' at the bottom was a quote reading, "Everything is the way it's supposed to be." ~Clockwork On either side of the picture was an older and a younger version of the man.
"So...his name is Clockwork?" Flash asked.
Before they could look further, the book was suddenly surrounded by a bright green light. After a moment, it disappeared in a flash of light. As they watched, the other objects vanished in the same manner.
J'onn spoke,"I believe our patient is awake."