A/N: A big shout out to Classic Cowboy and his story Harry Potter and the Children of the Atom. With Classic Cowboy's permission, this story borrows elements of his story. Originally, this story was published under my old account, ThePandimensionalStoryteller.

Chapter 1

The young wizard, Harry Potter, sat in the usual compartment that he and his friends took on the Hogwarts Express as it steamed its way to the school. He sat there drifting in and out of consciousness as the long trip took the little bit of energy he had left in him. Lately, he has been feeling a great deal of exhaustion. The most likely cause of this exhaustion was the recent series of events that happen over the course of the year.

Though knowing there was one more person that cared about Harry gave him happiness, this happiness was also tainted with fear of potential loss. Harry worried about Sirius's, his godfather's, safety. The dark hooded beings known as the dementors were always on the hunt for the escapees of the dreaded prison called Azkaban.

Then there was Voldemort too, especially with the Death Eater riot that happened at the Quidditch World Cup. At the moment, such thoughts were fading as Harry finally gave in to his body's urging to rest. Still, despite these recent being perfectly adequate to explain his exhaustion, Harry suspected something else. At the moment, he couldn't put his finger on it. As Harry tried to get some rest, he was interrupted by an explosive debate.

His friends, Ron Weasley and Hermione Granger were embroiled in a lengthy debate. It was a debate dealing with the civil rights of a newly discovered group of people called mutants. Mutants were people whose genetic code has mutations that give them extraordinary abilities. Very similar to the abilities of magic folk, though being non-magical in scope it seemed.

Unfortunately in this day and age, mutants are feared and hated by both muggles and magic folk. The debate between Ron and Hermione has been going on for an hour and a half now.

"I CANNOT BELIEVE YOU WOULD SAY THAT RON! LET ALONE THINK IT! I mean, haven't you consider how bigoted that is?!" raved Hermione.

"They don't belong in our world. Let them stay in the muggle world. After all, it would give us a lot less trouble." Ron said with a little bit of venom in his voice.

He turned to Harry and asked, "You agree with me don't you Harry?"

Harry wasn't sure to think. He still wasn't fully aware of the details, but he did recall that during the summer a news report coming from the United States. The report featured a mutant terrorist attempting to overtake a nuclear silo. The terrorist was reported to have the ability to make magnetic force fields and manipulate metal.

Due to the threat of nuclear annihilation, news of this had even reached the deepest depths of the wizarding world. There is no magic that can defend against such a threat. The situation caused a wave of anti-mutant hysteria everywhere. Harry remembers his nasty aunt and uncle commenting on the report. The things they said were akin to what racists say about other ethnic groups.

To Harry, that sort of unpleasantness was like a wildfire. Paranoia was at an all-time high and has brought about deep-rooted prejudice. So far no witch or wizard had been ousted as a mutant. However, the only question Harry had was: How could anyone tell the difference between a mutant and a magic-user?

Harry could see why Hermione was upset with Ron and his attitude. She herself is a target of a similar brand of bigotry due to her own heritage.

"Sorry Ron, but I'll have to go with Hermione on this one. After all, could you imagine being in their shoes?" Harry said rather bluntly.

He really didn't want to get wrapped up in the debate, but he knew Ron would counter harshly.

"Mutants are freaks of nature for crying out loud! I mean bloody hell! The best thing for us and muggles is to lock them up somewhere!" Ron said with anticipated harshness.

"I wouldn't wish that on anyone, considering that I was locked away by people who were afraid of me," Harry said quietly, once again nodding off.

Ron and Hermione were both taken aback by this. For the remainder of the trip, the trio stayed quiet. Things did get a bit heated, but all three knew that those same things would cool off soon. However, what was to come wasn't part of that plan.

Harry, despite being in a deep sleep, started to hear voices. Rather angry voices at that. The funny thing is, it was Ron's and Hermione's voices. Not only did he hear the voices, but he felt the emotions at the same time. The full force of two sets of emotions and thoughts collided with his mind. Then a sharp pain rang throughout his brain as if a thousand sledgehammers slammed into his skull.

"AHHHHHHHH!" Harry screamed out in pain and then blacked out.

Later, in the dark and castle-like corridors of Hogwarts, the headmaster, Professor Albus Dumbledore, made his way to his office. Two days ago, he and the other staff had to deal with Harry's sudden emergency. After investigating the incident, he and his colleagues concluded that this wasn't the work of Voldemort.

In fact, this was different altogether. The infirmary staff stated there was no magical cause to Harry's sudden blackout. Whatever had attacked the boy, Dumbledore knew that this was out of his league. He knew that Harry was undergoing a change and that he was vulnerable now. The most he's been since he was an infant on that fateful day when his parents were murdered.

Fortunately, Dumbledore enacted a plan in order to get Harry the help he needed. Looking out of one of the many stained glass windows that lined the corridor he saw a fog rising and growing thicker. "They're here," Dumbledore said to himself and proceeded to his office.

Inside he found two figures. One, a bald man in his early sixties sitting in a powered wheelchair. The other man was in his mid-thirties with dark brown hair. The younger man wore unusual eyewear marked by a crimson streak of light that lit up the room.

"Good evening Charles, I dare say you are one of the few people who could enter my office without my approval. How are you old friend?" said Dumbledore in a kindly and warm manner with his hand extended.

"I'm doing very well Albus, this is my associate Cyclops." said the bald man as he took Dumbledore's hand to shake it. He then gestured to the younger man to his right. Cyclops proceeded to offer his hand to Dumbledore's to shake hands.

"Nice to meet you. Now, with the pleasantries out of the way, I'll get to the point Charles. You couldn't have come at a better time. I believe Harry has displayed mutant powers. He had lost consciousness while on the Express and has been comatose for the past two days. He's stable, but I fear he's in great danger now." Dumbledore explained.

The bald man, Professor Charles Xavier, was well aware of the situation. He had been briefed by the urgent letter sent to him by Dumbledore. Plus, Xavier's supercomputer, Cerebro, confirmed this as well. Cerebro detected a spiking energy signature that was evident when a mutant 'discovered' their powers. Xavier hoped that this energy signature wasn't detected by anyone else. Luckily, he got here first to ensure that the young man got the help he needed.

While his friend took all of this information in, Dumbledore took his seat at his desk. With the wave of his wand hand, the glow of the fireplace brightened. The yellow-orange flames painted light throughout the room.

"Please take a seat." Dumbledore offered Cyclops, who remained silent as he took a seat.

Finally, Professor Xavier spoke, "Albus, would it be possible for me to speak with him in person?"

The headmaster's brow drooped a bit.

"He's still unconscious, Charles," Dumbledore said.

"Please, show me the way Albus," Xavier said in a kindly, but serious manner.

In the infirmary, Harry was tossing and turning violently in a dark and cold place. It felt like the Dementor's Kiss. He was a prisoner of his own mind. All of the negative thoughts, the painful memories flooded his mind's eye. No matter how much he turned away, another evil made itself known.

The thrashing started to become real as Harry's body tossed on the bed. Madam Pomfrey rushed to his bedside. The seizure had come about suddenly and was getting worse. No matter what she tried, none of the spells would work.

In the nick of time, Dumbledore and Xavier entered the room with haste. Xavier sensed the inner conflict within Harry. Now, Xavier began his work despite the Matron's protests.

"What are you doing! Can't you see there's an emergency!" Madam Pomfrey yelled in anger.

However, Dumbledore assured her that Xavier was the only person who could help Harry.

"My dear lady, my friend is the only one who can save him now. Please allow him to work." the Headmaster said calmly.

Soon, Xavier placed his hands on either side of Harry's sweat-drenched head. He closed his eyes and concentrated. Harry was screaming a soundless scream as his bad memories overtook him. He was feeling paralyzed and being drowned at the same time. Darkness surrounded and constricted him like an anaconda, slowly tightening its grip.

"DIE HARRY POTTER! DIE!" shouted an eerily familiar voice.

Just as the walls of his mind started to collapse, a bright flash of soft yellow light filled his mind's eye. Another unworldly, but much kinder, voice filled his mind's ears.

"Harry, do not be afraid. Focus on my voice."

Gathering new strength, Harry joined with the other force. Together they pushed out the darkness and sealed it away from his mind.

Soon, Harry found himself awake. His weak eyes could barely focus, but he made out an older, bald man sitting next to his bed. The man handed him his glasses off of the nightstand. With his glasses on, Harry saw the bald man more clearly as well as Professor Dumbledore sitting on the next bed over.

"Good morning Mr. Potter. It would seem that you've had a very troublesome night," said Xavier.

"Was...was that a dream?" he said groggily.

"I'm afraid not. You were telepathically attacked," answered Xavier.

It was clear to Harry that this man was the one who helped him through the horrifying experience.

"Harry, how are you feeling now?" asked Dumbledore with much concern in his voice.

"A little better considering that nightmare is over," Harry said with some relief knowing he was safe.

"You can rest easy now. This is Charles Xavier," Dumbledore said, introducing the two.

"I wished we could have met in better circumstances," Xavier said as he shook Harry's hand.

"Thank you," Harry said in gratitude.

"You're welcome. When you are able and ready, your Headmaster and I have much to discuss with you," said Xavier.

Harry nodded and soon felt the urge of his body needing more rest. As soon as he fell asleep, Dumbledore and Xavier left the infirmary. Both of them were quite tired staying up all night helping Harry break free of his mental prison inflicted upon him by an unknown assailant.

On the outskirts of the school grounds, the fog from yesterday concealed a rather large jet. The Blackbird, as it was called, was an impressive achievement of technology. Currently, it was housing three. Cyclops from earlier, and two others.

One was a beautiful woman with silver-white hair, blue eyes, and of African descent. Her codename was Storm. She was also responsible for the fog that surrounded the Blackbird.

The other was a short and burly, unshaven man wearing a 'Batman'-like a mask. This was Wolverine. He was asleep on one of the bunks on the jet, snoring quite loudly.

"Cyclops, has Charles made any progress with the boy?" Storm asked.

"Yes. Charles managed to pull the boy out of his coma." Cyclops replied.

"That's good." Storm said with a sigh.

"By the way, has Jean called?" Cyclops asked. He hoped to hear from his wife.

"Jean has indeed left you a message," said Storm with a smirk.

With a slight laugh, Cyclops responded "Oh the joys of marriage."

As Cyclops passed by, Wolverine woke up with a loud snarl. The tired and grumpy wildman stood and stretched.

"Has Chuck finished with the kid yet?" asked Wolverine.

"The professor was successful, but he wishes to give the boy some time to rest." Storm answered.

Wolverine muttered something rude under his breath. He hated playing the waiting game. While he didn't mind the peaceful scenery, or what little he could see through the fog anyway, he was itching for a fight. However, it would seem that wasn't an option.

"Well, I'm goin' out for a smoke," Wolverine said as he made his exit.

Storm sighed. 'Typical Logan' she thought as she picked up a book to pass the time.

Back at the infirmary, Harry awoke to find Hermione sitting next to his bed. He wasn't sure how long he'd been asleep.

"Harry, you're awake!" Hermione said happily.

She and Ron had been worried about Harry's condition since the incident on the Hogwarts Express. Ron couldn't join her due to having detention after participating with his brothers, George and Fred, in a prank. Neither of them knew the extent of the whole incident, though Hermione suspected there was more to it.

"Yeah and doing much better now. Professor Dumbledore had to bring in someone to help me, a bald man in a wheelchair." Harry said with renewed energy.

"Well, that's unusual that Professor Dumbledore would call for outside help." said Hermione.

A cold thought entered Harry's mind. Hermione thought the same thing too. There have been times, especially lately, when she knew exactly what Harry was feeling and thinking. However before anything more could be said, Madam Pomfrey shooed her out of the infirmary.

After returning to the Gryffindor dorm, Hermione remained in deep thought. She had a fairly good idea who it was that came in to help Harry. Her Uncle Hank, her mother's older brother, was an accomplished biochemist who worked with Charles Xavier, who matched Harry's description of the man who helped him.

Hermione had read some of Xavier's work and his advocacy for mutant civil rights. Since the mutant terrorist incident over the summer, she began to wonder if magic folk and mutants had a similar basis for their powers.

Such thoughts were widely condemned in the wizarding world. Anything suggesting muggles, magic folk, and mutants were all part of the same human evolutionary tree was deeply frowned upon by all sides. Of course, there are exceptions to this cruel train of thought. Xavier being one and herself being second.

Considering the whole situation, Hermione simplified her thoughts and asked a simple, but extremely important question: 'If it was Xavier, then why is he here?'. After all, Very few muggles knew about Hogwarts or even the wizarding world at large.

Obviously, Hermione figured, Xavier and Dumbledore knew each other. That would explain how he could get here. That didn't explain why Xavier would be called on to help Harry. Given the facts, she hypothesized an enlightening but unfortunate conclusion.

"What if Harry's a mutant?" Hermione said quietly to herself.

If her line of thought is true, then this could have dire consequences. 'Whatever happens, they will cross that bridge when the time comes,' she thought. Hermione proceeded to go do her homework with her fellow house-members.

In Dumbledore's office, a secretive staff meeting is underway. Xavier was greeted by the full manner of strangeness that surrounded the staff. However, he wasn't too much of an outsider to this sort of eccentricity. One of the teachers at this school gave him a jarring feeling. A tall, dark imposing figure with long black hair and sharply hooked nose stared at the mutant professor with contempt. Despite this, Xavier wasn't undaunted.

'Staring is rude, you know' said Xavier telepathically to the figure.

The figure was shocked by this but quickly regained his composure. Once all of the teachers took their spots, Dumbledore introduced everyone to Xavier.

"Now, as you are all aware, two days ago an emergency with Harry Potter occurred on the Hogwarts Express. Due to the nature of the emergency, Mr. Potter will be transferred to Professor Charles Xavier's school for his protection." Dumbledore told the staff with his usual confidence.

He was careful to avoid the topic of Harry being a mutant. There were many professors who didn't see eye-to-eye with him or Xavier.

Xavier sensed the unease in his friend. Dumbledore hiding information wasn't something that set well with his nature. However, Xavier knew from personal experience what the consequences would be if knowledge of Harry's mutation were known.

"Professor Xavier, what do your students learn at your school and what is its purpose?" asked a stern woman wearing a crooked witch hat and emerald robes.

While Minerva McGonagall was a trusted friend and colleague of Dumbledore's, she had never even heard of Charles Xavier until yesterday. Judging by the suit he wore, it was obvious he came from the muggle world. She suspected that this man wasn't a mere muggle though. Xavier picked up on McGonagall's thoughts.

"My school is very similar to your own. We teach our students to learn about their gifts and how to control them. Also, our school provides our students with a sense of belonging. We're dedicated to making the world a better place." Xavier said in a very tactful and warm manner.

In his characteristic calm and endearing voice, Xavier successfully put McGonagall at ease. She may have been a bit harsh. Once she witnessed how Xavier carried himself, McGonagall was sure that this man could be trusted. Much to Dumbledore's delight, he was glad to see that his old friend still had his own brand of 'magic' when it came to speaking to people.

Afterward, there was much more discussion about how to make arrangements so that Harry could continue his courses here as well as being transferred to Xavier's school. The meeting went much more smoothly. However, through the cracks in the walls, the ears of a ne'er do well was taking note of the meeting. He didn't like what he heard one bit!

Returning to the Blackbird, Xavier saw Wolverine standing outside the jet's loading ramp smoking. Xavier disliked Logan's habit, but at least Logan had enough respect to go outside to smoke away from students.

"So, are we ready to go Chuck, or are we going to have another slumber party?" said Wolverine sarcastically.

"Unfortunately my friend, the mission has changed a bit. It's going to take two weeks for the proper arrangements. Which means Harry must be protected while he remains here…" Xavier was interrupted.

"SO, I guess I'll be playing babysitter for the runt. " Wolverine said, not much pleased with the whole situation.

Xavier knew that when dealing with Wolverine, you have to take things in strides.

"Of course, you're the best at what you do, Logan," Xavier responded with a sharp wit.

Wolverine caught on to the professor's tone and gave a small grin in amusement.

After grabbing his backpack and civilian clothes, Wolverine took his instructions from Xavier and headed off to the Gryffindor Tower where he would meet with Professors Dumbledore and McGonagall. Psylocke would be there in a couple of hours.

Until then, he would be on his own. Walking up to the castle, Wolverine took in the sights. While he wasn't much into architecture, he was impressed with the ramparts of Hogwarts. It took him a minute to get his bearings, but using the mental map Xavier had given him, Wolverine found his way to Gryffindor Tower.

Nearing the entrance of the tower, Wolverine gained the attention of several students as they made their way to their mid-day classes. Most weren't sure what to make of him, but it was clear that he was someone not to be tampered with.

Even Peeves avoided the newcomer and he's been dead for centuries. Of course, the feral Wolverine preferred people avoiding him. The scents of this castle were a bit overwhelming for him as he marched into the right direction. The wetness, the smoke from torches, and the failed potion experiments lined his nostrils.

The one smell that was somewhat familiar to him was the typical scent of teenagers. Under his breath, Wolverine growled. The scent reminded him of the sorts of trouble the students at Xavier's would get into when he wasn't there.