Disclaimer: I don't own Naruto or X-Men: Evolution.

A/N: OK a double post to finish the third season. So read Chapter 30 first. I'll be doing a mass update of all stories for Christmas next then focus on finishing this story out. I'll also try to do an O.C chapter since season 4 is only 9 episodes long.

Beta: Jebest4781 and Chaos-PSD.

Chapter XXXI: Dark Horizon.

Last Time.

She started to cry into Logan's chest before seeing S.H.I.E.L.D.s helicopters. "Go. We'll handle them. If you ever need us, throw this." Naruto said handing X-23 a Hiraishin (Flying Thunder God.) kunai. She turn to run, missing a chip land on her collar. A small helicopter like the XM-Velocity following after her with Lady Deathstrike grappling up to it.

Fury walked up to them before Logan spoke. "Leave her, she's been through enough." Logan said as Fury put his hands on his hips. "I can't just let this go!" Naruto sighed before Logan spoke. "Yes you can, and you will."

The Next Day.

Naruto sat on the bay window in Rogue's and Kitty's room with Rogue sitting between his legs braiding her hair as she leaned against him. Charles and Wolverine came in and spoke. "I was worried when I saw your weren't in the infirmary." Charles aid as Rogue looked to them.

"It's okay, Professor. I feel fine, really." She replied as Wolverine smirked. "Better enough to join the training?" She started to sweat before speaking. "I-I don't think I'm that well." She replied waving her hands. "I'm sure you'll like this one." Wolverine said picking up a bag of dodgeballs.

Naruto smiled out of the window remembering Logan saying he's not going to push the kids after witnessing what his daughter went through.

Later.

On the other side of the mansion, Ashura brought Scott, Rachel, Charles and Kurt into a study. "Why are we here?" Rachel asked crossing her arms under her bust. "To meet a friend. He wanted to meet only a few of you at the moment. So please, don't tell the others yet." Charles brought his hands up and laced his fingers.

"Is this the person who's been here all day?" Ashura nodded before Leo walked out of the shadows. "This is Leo. He's a person who got reincarnated into a turtle that got exposed to some ooze that mutated him." Leo waved showing them his three fingers. "Hello."

Now.

Xavier's School For The Gifted, Middle Of The Night.

Kitty woke up from the sound of a pained groan. "Scott?" She asked getting up and moved to the door. The door handle turned having her gasp and hid against the wall. The door opened and she phased to the outside and ran to Scott's room. "Scott." She whispered trying to wake Scott up.

He only groaned before the door opened. Kitty ran to Kurt's room and tried waking him up. When he didn't someone touched her, causing her to gasp and fall down. The moon lit the room revealing Rogue who picked up the unconscious Kitty and placed her back on her bed.

The next morning, Naruto walked into the kitchen, planning to talk with Logan about X23 and how they were going to help her out. He walked in the kitchen before seeing that no one was inside, nor were there any dirty plates in the sink. He raised an eyebrow before looking at the clock. '8:40.' "Did I miss a party last night? Or is there no school today?"

He asked before the others hurried into the kitchen knocking him over. He looked up, only to faceplant as Kurama jumped on his head. "Why the hell are you all just now eating?" He asked as Rachel rubbed her eyes, walking in, her jeans hanging loosely off her hips showing the bands of her thong.

"Everyone overslept." Kurama narrowed his eyes before sniffing the air. He turned and jumped on Naruto's back before running outside. "Someone else was here last night." He said running to the trees. He sniffed a tree before looking down and saw two sets of footprints. One belonging to a man, the other a woman by the smaller size.

Later, Bayville High.

The X-Men rushed inside as Rogue, her hair braided and pulled to the front walked the halls. She's wearing her track pants and her green hoodie. Once all but her went inside, Rogue stopped and turned to see a limo stop and open its door. She walked over and got inside.

Inside, Naruto walked with Scott, Emma, and Jean who sighed. "Kind of sad, isn't it? It feels like we've been here forever." She said as Naruto looked at the graduation banners. "Good riddance, I can't wait until tomorrow. Nor buy the yearbook." Scott said passing Kelly's office.

"Rest assured, the feeling's mutual Mr. Summers." Kelly said standing by the door. "Just make sure there's no Mutant Mischief." Naruto just stared at him before turning around. "Just make sure you give us our diplomas." Naruto said while wrapping his arm around Jean's waist as Scott did the same to Emma.

Brotherhood Boarding House.

Rogue walked to the door and and opened it before grabbing Todd, absorbing his power. She ran over and did the same to Fred and Lance. "What's going on?!" Pietro asked before seeing Rogue levitating. He tried to run, only for Rogue to levitate him and brought him over to her.

Outside, Mystique walked out of the limo and opened the door, allowing Rogue to walk in.

Xavier's School For The Gifted.

Rain came down as Ororo looked out the window. "I'll make sure your big day tomorrow will be sunny." Jean walked in with hot tea and set it down on the table. "Thanks Storm, I want it perfect tomorrow for my fami..." She trailed off seeing Rachel straddling Naruto's waist on the couch making out with him.

Rachel moaned as Naruto grabbed her ass before Charles spoke. "(Ahem) Any thought of what you'll do after?" Jean nodded before handing him a cup. "Yes, I'm thinking medical, or Genetics. I know a great teacher." Ororo walked away from the window, missing Rogue walking past it.

Warehouse.

Rogue looked up to see an open window before turning to Mystique. "The window." Mystique sighed before holding her hand up. Rogue grabbed it before walking out and transformed into an Owl. Flying in, she saw Colossus in his metal form holding a crate. She touched him causing the crate fall on both of them.

Rogue broke them out, and threw Colossus aside before Sabretooth tackled her. Metal covered her arms to prevent a strike from him, absorbing his power as well. "Awfully bold of you coming here. Especially on your own." She turned to see Pyro with flames around him. He shot fire at Rogue who had metal cover her frame. Her coat burned off before she grabbed Pyro.

Gambit walked to her, twirling his staff. "Well done, Cherie (Sweetheart). Look's like the Rogue's up to no good. I like that in a woman." He said as Rogue went back to normal and walked towards Gambit. Gambit walked backwards and held up his staff. "But you're not in this alone."

"Who's behind this? Mystique?" He asked jumping from a swipe. "I think so, but why?" She lifted him up and threw him to a wall before jumping at him. "See if you can guess." She said as he used his feet to keep her away. He threw her away before getting up. He turned around and she kissed him, absorbing his powers.

Later, Magneto walked in and saw his men unconscious before stopping at Gambit. "Rogue, where are you?" He asked before seeing another Gambit across the room. The Gambit beside him transformed into Rogue who reached up to touch his face.

The Next Day, Bayville High.

The graduates stood on the football field in maroon robes and hats. "Aren't you happy?" Rachel asked standing in front of Naruto. "Happy to be rid of school." She raised an eyebrow at that. "No college?" She asked as he laughed. "Ha-ha-ha-ha! That's a good one. No, I don't need college, I'm doing fine now."

"I'm still getting royalties from my books, I've got you and the other ladies in my life. What more could I ask for? Plus, I can visit my world for up to a week now before the chakra from the Reverse Summon runs out. Still can't believe only three years went by for them." Rachel shrugged at that. "Each World travels at it's own pace."

"Yours probably goes slower than ours." She reached up and gave him a chaste kiss. Jean walked over before her parents and little sister ran to them.

Later, as Kelly was giving a speech. Magneto, his Acolytes, and the Brotherhood minus Lance walked to the field. Everyone but the X-Men ran away before Magneto spoke. Suddenly, Pietro dashed in with Rogue.

She's wearing a dark purple halter top, long purple gloves that come up to about her shoulders, and a knee-length skirt covered with a white chain that hangs around her waist. Knee high boots, and a light purple scarf.

Suddenly, the chairs floated around her as Charles spoke. "What's the meaning of this Erik?" Magneto looked back to him. "Nothing Charles, Rogue is being used by Mesmero! She came to our base and took our powers! She took the Brotherhoods and all of yours as well! Mesmero erased the memories."

Rogue threw the chairs at them before flying away. "ANNA!" Naruto yelled running to where she was. He growled before walking back to the others. "Logan, track her." Charles said as Magneto looked to Gambit and Sabretooth. "You two, go with him." He said to them.

"No way am I trusting-!" Logan was interrupted by Naruto who spoke up. "I'll go with them." He took off his robe and hat before walking to the parking lot. "Girls, I'll go alone, I don't want to fight all of you if Mesmero goes that route again like last time."

Later, Naruto wearing his leather jacket followed behind Logan, Sabretooth, and Gambit on motorcycles driving in the direction Rogue flew off in.

Xavier's School For The Gifted.

"We need to keep Rogue from getting the last key. And if we fail..." Charles trailed off rolling to the computer with Magneto. "We find the door, and defend it. But we'll need to use our most experienced members." Charles nodded at that as Beast was typing on the computer.

"To prevent Mesmero from taking anyone else under his control, I'll need to add mental blockers to them all." Magneto nodded at that before Beast spoke up. "I've had little success targeting Apocalypse's place of origin beyond Ancient Egypt." Magneto leaned down before speaking.

"Try his real name. En Sabah Nur." Doing that, hieroglyphics came up with a man with blue lines on his stomach and face came up. "En Sabah Nur. Ruler of Giza over five thousand years ago. So it makes sense that's where his tomb would be." Magneto sighed before speaking.

"Mesmero would probably know the exact place." Charles sighed before rolling to Cerebro. "I was in his mind, but I'll need to use Cerebro to clean the memories up."

Airport, Naruto, Logan, Sabretooth, And Gambit.

The group found the limo just outside the Airport beside the bay. "They were here." Naruto said seeing Rogue's clothing on the floor. Logan and Sabertooth started to argue. Only to stop as red chakra surrounded Naruto. "ENOUGH! We are on the same side here! We need to stop Apocalypse together or we will all fall."

"They may have taken a boat." Sabertooth growled as a plane descended to the Airport. "Or a plane." Gambit said before they walked to the airport. They went to the tower and saw the workers knocked out before Naruto went to the radar. "One just left here passing California, and is heading to the Pacific." He said looking at a spot on the radar.

"I hope you have your frequent flying cards." Gambit said looking at a private jet.

Giza.

The X-Men landed in front of the Sphinx as Magneto, Colossus, Pyro, and Quicksilver walked out of their orbs. Phoenix looked at the Sphinx and shivered. "Something wrong?" Emma asked walking to her with Scarlet Witch. "I... Remember hearing about Apocalypse when I was possessing someone at the time."

"I was a little afraid." Phoenix replied as Kitty put on a oxygen mask that covered her entire face and a flashlight. She jumped up and phased into the ground and after a minute, she opened the door under the Sphinx allowing the others to walk down the steps. Once they got to the bottom, Kitty sat on the bottom steps, knees pulled up to her chest.

They walked around and saw statues to the Egyptian gods before their eyes opened up and started to attack the group as the doors closed back up. The group teamed up into pairs to attack the statues as the floor started to give way and forced them to split up to go into other rooms.

Magneto, Charles, and Beast went into a room with no statues before Beast put on a headset to communicate with Storm. They walked in a room with Hieroglyphics written all over the room and pillars. Beast did his best to translate the ones he knew. He explained a Pharaoh, Rama-Tut, fell from the skies with advanced technology and became the Pharaoh.

And an infant grey-skinned mutant was abandoned and was taken in by a group of thieves with the leader adopting him seeing great power in the baby. "And named him En Sabah Nur. En Sabah Nur grew to be a powerful warrior. Rumors of En Sabah Nur's power reached Rama-Tut who saw him as a threat."

"And he attacked the group in hopes of killing him. But En Sabah Nur survived the attack. And since nothing could stop him, En Sabah Nur took the name, Apocalypse." 'Professor, the statues are robots!' Charles heard Cyclops in his head. "Apocalypse went after the Pharaoh." Beast continued to read.

"Who fled, never to be seen again. Apocalypse soon found that the source of Rama-Tut's power was a vessel in these chambers. And inside the vessel was a device called 'The Eyes of Ages'. He mastered the secrets of it, to reshape the World in his own image." Charles looked down before speaking.

"Mutants. He's going to turn humans into Mutants. All humans." Best looked back and continued. "When Apocalypse activated it, it drained him of almost all of his life force. And it was then he was betrayed by his followers, fearing the future he would have made. They sealed him inside, and buried him in the highest part of the World. Locked behind three doors."

Tibet.

The group looked at a plane as snow fell down and the wind blew hard. "I've got footprints!" Naruto yelled walking up a path. Logan radioed Beast where they are as they walked up the mountain

Up ahead in a cave, Mystique walked with Mesmero and Rogue who's in her winter clothes. They made it to the last door holding Apocalypse. "The day has finally come." Mesmero said before turning to the women. "Now, the last key. The shape-shifting Mutant, Mystique."

She gasped before glaring at Mesmero. "You told me Rogue was the last key! Why did you lie to me?!" Mesmero lifted a staff before pointing to the door. "You both are needed to open the door. Apocalypse will not forget those loyal to him, just go through there." He pointd to a small hole.

"Why not brainwash me like you did her?" Mystique asked pointing to Rogue. "Because your mental powers are too strong." She just stared before transforming into a King Cobra and slithered in. A moment later, the door opened showing Mystique was turned to stone before Mesmero pointed ahead having Rogue walk forward.

She went down a set of steps to a coffin that opened up showing an elderly man in Ancient Egyptian clothing. She pulled off a glove and held it out.

Upstairs, Naruto ran in and crashed through the door. Logan went to Mesmero with his claws before slashing at him. Only to reel back as Mesmero's staff shocked him. Naruto dropped down with a Rasengan (Spiraling Sphere.) and hit Mesmero in the chest, sending him flying back into a wall and through it.

"That was for Rogue, you bald son of a bitch!" he growled out at Mesmero's unconscious form. Logan dashed to the stairs and down towards Rogue. Rogue was lying unconscious as Apocalypse was floating up and glowing a bright white.

Logan dashed to him, only for Apocolypse to clench his fist and had Logan fly back to his coffin. Naruto walked down the stairs and saw Apocalypse before speaking. "Where. Is. Rogue?" He asked as Apocalypse just stared at him before Naruto was sent to the ceiling and sent down to the floor hard.

Naruto groaned in pain before getting up and picked up Rogue, bridal style. He heard the others as well as the group who went to Giza getting beaten before walking up the stairs. "Our greatest battle has yet to begin." Charles said laying on the ground before they felt immense power.

A golden glow covered the area before they looked to see Naruto walk out of the chamber.

He's covered in yellow chakra, which emanates from him reminiscent of flickering flames. He has two horns on his head, six magatama markings around his neck, a swirl over his stomach and various other lines extending along his body. They saw that his eyes were orange.

"Yeah, but he made the mistake of using my loved ones for his plans. That's not going to fly with me." Naruto said walking up to them as Logan followed.

To Be Continued.

A/N: Thanks for reading and let me know of any mistakes.

Beta: Jebest4781 and Chaos-PSD.

Like I said up top, after a mass update for all stories for Christmas, I'll be focusing on this story to finish it out.

Talk To You Later,

Lone Wolf Out.