Disclaimer: I don't own Naruto or The Avengers, Earth's Mightiest Heroes.

A/N: I decided on skipping the Purple Man Ep because it's A: A one-off Ep and doesn't get brought up again. And B: I despise mind control/manipulation. So for the future, I'll probably skip Filler/one-off episodes that deal with mind control. I'll go into slightly more in the bottom A/N.

Also, Korra won the poll as I had to end it due to not getting any votes for about a week or 2 and I'm focusing on this story to finish it out due to getting in the last 6 Eps.

Beta: Jebest4781, and Chaos-PSD.


Chapter XLVI: Code Red.

Last Time.

"Hank Pym is welcome back to the team any time. That's who we want."

"I told ya. The name's Yellowjacket." Hank said, pulling his mask up before walking away.

"Tony?"

Iron Man looked to Wasp and shook his head. "Absolutely not."

"He's your friend." She said as he sighed.

"Was. Yellowjacket is crazy as a hornets' nest, and a loose cannon to boot."

"I've been an Avenger from day one. I've always been a happy camper. I've never asked you for anything, Tony Stark, but I'm asking now. Take Hank back. We need him. I need him." Wasp said as Iron Man sighed before they heard J.A.R.V.I.S.

"Pardon me, sir. But the New York Police Department is reporting a throng of "Mole People" spilling from Madison Square Garden. And I don't believe there was a game today."

Yellowjacket then turned to them. "Bet I'd bag more Mole People than you do, Stark." He then flies away at that.

"Wait, what? Yellowjacket!" Iron Man said as he chased after Yellowjacket.

Now.

Avengers Mansion.

"United States Secretary of Defense Dell Rusk held a special press conference this morning, where he reiterated his stance on…"

Iron Man and Captain America were sparing in the training room as a report was on the TV by them.

"The Avengers. Some may call them heroes, but they're nothing more than a super-powered army, working above the laws of our government. They present a clear danger to hard-working American citizens, and I will be keeping a close eye on them."

"That's it. I'm crossing Dell Rusk off the Christmas card list." Iron Man said as Cap's shield hit the TV and bounced off showing it was protected.

"Iron Man. Keep your head in the game."

"You're telling me not to multitask? Not gonna happen." Iron Man said before he continues training with Captain America.

"Don't worry about Dell Rusk. Politicians come and go. The work we do lives on." Cap said running to the armored hero and threw his shield having Iron Man flip over it.

"Heh. If I said something like "The work we do lives on", it would sound corny. But coming from you, it's so natural."

"I'm full of surprises," Cap said backflipping away as his shield cut a pipe down and hit Iron Man into a wall.

Iron Man then got up and stared at Captain America. "See if this surprises you. The Avengers need a new leader, officially."

"What are you saying?"

"I formed the Avengers to get a job done, but something was missing until you came along. It took a while for you to catch up to the 21st century, but now that you're here, you are the face of the Avengers. You're the leader we need."

Captain America sighed at that. "Tony, I don't know what to say.

"Start with 'Yes'." Iron Man finished before the room shook as red mysterious gas released into the room.

Iron Man then looked to Cap as he started coughing from the gas that now covered the room. "Cap!"

"Warning. Toxicity levels of gaseous emissions are threatening armor integrity."

"I'm fine, J.A.R.V.I.S... What about Cap?" He asked just as Captain America walked to him, coughing, before leaning forward.

Iron Man catches Captain America before he falls and sees his face become red and his sclera turned black. Outside, gas spreads into Manhattan and starts infecting civilians.

Back inside, Iron Man flew Cap to the infirmary "J.A.R.V.I.S., prep the infirmary, seal the Mansion, initiate security lockdown, and patch me through to Thor." He said coming out of the elevator shaft. "Thor, you read me? We've got a situation at the Mansion."

"What madness is this?"

"That cloud is toxic. Get rid of it before all of Manhattan is exposed."

"Consider it done, my friend."

Outside, Thor pulls the cloud into the air with Mjölnir and flies away with it.

Inside Shinobi, Black Cat, Panther, and Wasp stood with Iron Man looking over Captain America. "Body temperature is at 104 and climbing, and his heart is beating erratically." Panther said crossing his arms.

"He doesn't have long, guys."

Iron Man then looked to the others. "He's not the only one. We don't know how many of us were exposed. J.A.R.V.I.S., analysis of this virus? Anything in your data banks?"

"Nothing, sir," J.A.R.V.I.S. replied as Captain America tosses in his bed.

"Easy, pal. Try not to move."

Captain America opens his eyes and sees his reflection in Iron Man's helmet. "Oh no. Not this. Not him."

Wasp and Black Cat then held their head. "Ooh. I don't feel so hot."

Black Panther and Naruto catch the two and carry them to a bed. Naruto saw Cat's skin turn red as she groaned. "Easy dear," Naruto said holding her hand.

"It may be just a matter of time for all of us, not to mention anyone exposed on the streets outside. We need samples from them. From there, we may be able to use them to synthesize an antidote." Panther said before J.A.R.V.I.S. spoke up.

"Sir, incoming call. Secretary of Defense Rusk on secured channel alpha."

"Rusk? He wants to talk now?" Iron Man asked as a screen turned on showing a Caucasian Man with brown hair, graying temples, and wearing glasses in a blue suit.

"You Avengers have finally crossed the line. Storing dangerous biotech weapons in the heart of Manhattan? This is precisely what I've been talking about."

"Mister Secretary, we were attacked."

"Tell that to the American people, Stark. This incident confirms what I've been telling them all along. The Avengers cannot be trusted. Now, I'm shutting you down until further notice."

"You know we can't do that. As for this "incident", we just need time to-!"

"Wrong answer. The die is cast. I'm officially taking matters into my own, more capable hands." Rusk said as a video of tanks parked outside the mansion came up.

Iron Man then turned to the others. "Let's get those samples into the accelerator for analysis. Rusk isn't giving us much time."

Black Panther looked to him before speaking. "The Wasp is fading fast, though Captain America and Black Cat are showing some resistance."

"The super-soldier serum," Naruto said as Cat opened her eyes and looked down to see her skin was red.

She pulled her hand out from Naruto's and covered her face. "Naruto… Please, I don't want you to see me like this."

Naruto smiled as his mask came down and moved her hands. "Felicia, I don't care about your looks, I love you."

"You're just saying that."

"No… Sure, the nice body, big tits, and rock hard ass help… Especially in this form as they grew."

"Heh, (Cough!) don't make me laugh."

"Felicia, I won't leave you except to go kick the person's ass that did this." Naruto finished leaning down to kiss her.

"Sir, an armored division has cordoned off the area, and the Mansion security systems are being hacked from the outside."

Iron Man looked up at that. "Hacked? I wrote those programs personally."

"A troop transport is landing on the front lawn as we speak.

"He's sending in troops? To do what, arrest us?"

Just then Doc Samson with a yellow visor gas mask and two men blasted through the door. The first is a muscular African-American man in a red and white suit and cowl with a yellow visor gas mask.

This is Falcon.

The next is a slim muscular Caucasian man with shoulder brown hair parted in the middle and a black domino mask with the gas mask. He's wearing a black bodysuit, brown boots and a holster and belt with black gloves, and a robotic metal arm up to his shoulder with a red star on it. He also picked up a rocket launcher.

This is the Winter Soldier.

"Code Red team, you have your objectives. Now move out." Winter Soldier said as Ms. Marvel floated down.

"I hope you guys have your invitations handy, 'cause we don't let just anyone in here."

Winter Soldier then aimed the launcher at her. "Here's my invitation." He then fires a rocket and hits the heroine. Who dropped to the ground.

She then stood up and looked at them. "I don't fall that easily.

Doc Samson dashed at her for a punch. "We'll see about that."

In space, Thor had just finished pulling the cloud before flying down. And was punched by a red Hulk in black shorts.

They fell on Liberty Island as Thor looked at the man. "You dare strike an Asgardian, mortal?"

The man just smirked. "That felt good. Let's do it again."

Mansion Med Bay.

Captain America woke up and hears distant booms. "I can't just sit this out." He said as he gets up.

Wasp looks over to the war hero and groans. "Cap, they're already working on an antidote. Besides, you're not going anywhere without me." She tries getting up, but falls off her bed."

"Wasp, no." Cap got up and put her back on the bed. "Stand down, soldier. You need to rest."

"You should heed your advice."

Cap looks to see the Winter Soldier in the med bay. "You look terrible. And certainly in no condition to deal with me."

"How about me?!"

Shinobi ran out of the shadows and punched the man in the face before they traded blows before Naruto caught his left arm. "Oh hey, you got a robotic arm as well," Naruto said before prongs came out of his knuckles, and he pushed his fist into the man's chest shocking him. "But I think mine's better!"

Naruto was then uppercut away as Winter dashed into him.

In the lab, Iron Man tries a sequence for the antidote that fails. "Come on, come on, we need that antidote." He said as Panther was beside him looking at another screen.

"Yes. It is taking more time than anticipated." He said before dropping down to his knees.

Iron Man flew over at that. "Panther, you okay?"

Black Panther nodded and stood. "I am fine." He said and removed his mask, showing his now mutated face.

"Oh no." Black Panther passes out having Iron Man kneel.

"Looks like someone needs a doctor."

Iron Man looked to see Samson leaning by the door.

"Samson!? Are you working for Rusk? I thought you were smarter than that."

Samson shrugged at that. "I'm under orders."

"J.A.R.V.I.S., some privacy, please?"

"Acknowledged." The doors closed, trapping Doc Samson outside.

"That'll hold him for a while. I hope." Iron Man said before Samson punches the door.

Outside, Ms. Marvel walks up to Samson. "Hey, doc! We're not done yet.

"You can't fight off the infection much longer. We're here to keep you all quarantined."

Ms. Marvel raised an eyebrow at that. "And who's we?" She asks before Samson knocks her down.

Thor VS Red Hulk.

CRACK!

"Have at thee!" Thor yelled as thunder roared and lightning cracked in the sky as he attacks Red Hulk, who dodges and grabs him

"Have at this!" Red yelled before he slammed Thor into the ground.

Thor knocks back Red Hulk and hits him with lightning.

Crack!

Red Hulk smiled as his eyes glowed yellow before he got up and attacked Thor.

Avengers Mansion.

Falcon flies into the training room and sees a hole in the wall.

"Looking for something?"

Falcon looked back to see Hawkeye with an arrow drawn in his bow.

"We're here to save lives, Hawkeye. Be smart and yours will be one of them."

"I'm healthy enough to deal with you," Hawkeye said before he fires the arrow at Falcon.

Falcon flies over and knocks down Hawkeye. "Falcon: You Avengers don't know when to quit, do you? Don't you get it? You brought this on yourself."

Hawkeye responded by throwing a sonic arrow tip that knocked down Falcon. "Ultrasonic arrow. Birds hate 'em. Now, what were you looking for in here?"

Lab.

"Sir I-!"

Iron Man spoke up to J.A.R.V.I.S. interrupting the A.I. "Take a message, J.A.R.V.I.S... The simulation's showing real progress against the toxin. Panther's out, and one of Rusk's hit squad is pounding on my door."

"I have an encrypted signal from Hawkeye, coming from the training room."

"That I'll take. Hawkeye, you hanging in there?"

"Barely. But I found the reason we're in this mess. It's an incendiary device, with a built-in emission system. It caused the explosion and released the airborne toxin all at once." The Archer replied over the speakers.

"Hold onto it. I'll do a scan and maybe we can figure out which psycho we ticked off this week."

"Hold on, Stark. I've seen this kind of tech before, in my days as a S.H.I.E.L.D. agent. This device is D.O.D. all the way."

"Department of Defense? So Rusk set us up. But why? Just an excuse to parade a second-stringer strike team?" Iron Man asked as he continued to type.

"I'm gonna leave that one to you. Have fun." Hawkeye said before he passed out, having started to mutate himself.

"Hawkeye, do you read me?"

Samson then breaks down the doors. "Forgive me, Iron Man. But we're taking control of these premises whether you like it or not. By order of-!"

He stopped as a mutated Ms. Marvel blasts him down. "Never turn your back on an Avenger with an attitude." She said and passed out as well.

"Carol, no! J.A.R.V.I.S., initiate the final sequence on my voice command. Go!"

"Processing. Sir, simulations are showing 4 symptom withdrawal based on your last antidote formula. Synthesizing now."

"Make it fast. We need it."

A few minutes later, getting the antidote, Iron Man injects Black Panther with the antidote. "Come on, let's go." Black Panther then returns to normal. "Yes!"

Iron Man then flies into the infirmary saw a downed Naruto whose skin was slightly red and cures Wasp and Black Cat before sticking Naruto. "Son of a bitch! I hate shots!"

"Cap!"

"Shaggy guy took him." Naruto groaned, rubbing his left arm before being tackled by Cat.

Pentagon.

The Winter Soldier drops Captain America at Dell Rusk's feet. "Winter Soldier, you have done much better than the rest of Code Red."

Winter Soldier nodded at that. "Thank you, sir."

Dell then looked down at Cap. "Hmm. You poor, misguided, outdated soul. You have no idea what this country needs from its heroes, do you? Don't you realize? This was all for your benefit." He said and kicked Captain America.

30 miles out, Iron Man is flying to the Pentagon. "J.A.R.V.I.S., I'm about 300 miles out from Washington, D.C., tracking Cap via his Avengers ID card. What's the status back at the ranch?"

"The afflicted Avengers are all responding to the antidote. Any affected civilians are also being treated. The only one left who hasn't been given the antidote is Captain America."

Iron Man sighed before speaking. "Not for long. I'll get to him in-!" He stopped as he saw Army jets by him. "Crap."

"Attention, Iron Man. This is Colonel Tom Parker, US. Air Command. We have orders to ground you immediately."

"Colonel, I respect that you have your orders and I have no intention of engaging you, but I also have no intention of letting my friend die. So if you'll excuse me." Iron Man said over his comms before he flies away with the jets following. "They've got me boxed in. J.A.R.V.I.S., lock onto Cap's ID signal. Give me a targeting solution."

"Target locked. But from more than a hundred miles out, you can't possibly-!"

Iron Man stops flying and raises his arms. "Eat your heart out, Hawkeye." He then fires a missile that delivers an antidote towards Dell Rusk's office, but Winter Soldier catches it in midair.

Dell just laughs at that "How perfect. The last attempt at salvation, gloriously thwarted by the most unlikely of adversaries." He then hits Captain America. "Now... Now I can savor this moment. I've waited so long."

Captain America attacks Dell by grabbing him "Show yourself, coward!" He then rips off Dell Rusk's skin, revealing him to be the Red Skull who knocks him down. "Red Skull."

Red Skull smiled. "And so, we have come full circle, Captain America." He then attacks Captain America with several punches. "I will crush you and everything you hold dear under my heel." He then picks up Captain America. "And now, for my final victory." He walks over and brings Captain America to Winter Soldier. "The ultimate irony. Finish him. Do it."

The Winter Soldier just looks down before he injects Captain America with the antidote.

"No!" Red Skull yells as he points a gun at the Winter Soldier. "Through your defiance, you have signed your death warrant."

A healed Captain America knocks the gun out of Red Skull's hand. "Look at me, Skull. You and I still have a score to settle."

Red Skull fires at Captain America, who blocks and tackles Red Skull outside through the window. Red Skull reaches for the gun, but Captain America stops him and holds him up, then knocks him down as Iron Man lands, followed by reporters.

"Nice photo op."

Captain America jumps back into the office to find the Winter Soldier gone and then picks up an empty antidote syringe.

Hydro Base.

At a S.H.I.E.L.D. hydro base, Shinobi, Hawkeye, Thor, and Wasp watched Samson, Falcon, and Red Skull be escorted inside as Iron Man walked to them. "Just spoke to the S.H.I.E.L.D. psych team. Falcon and Samson are gonna be treated for whatever mind control the Skull had them under."

"Good. They're not the bad guys." Wasp said as Thor held Mjölnir.

"Except for the red monstrosity I did battle with. He has not been seen since."

"Speaking of which, J.A.R.V.I.S. reports that the news footage of Cap and the Skull on the Pentagon lawn is being played worldwide."

Hawkeye crossed his arms at that before speaking. "Well, I hope they're looking into exactly how a psychopathic Hydra war criminal could get appointed Secretary of Defense. Uh, I'll never understand politics."

Iron Man shrugged before he too crossed his arms. "The important thing is that all of Rusk's public campaigns against us end up looking like the rantings of a madman. That's good PR for us. And we owe it all to this man." He gestures towards Captain America, who's looking out into the ocean.

Wasp looked towards him before speaking. "Cap?"

Iron Man stopped her before she tried to walk over to the war hero. "Let him be, Wasp. After all, he's been through? I just hope he hasn't forgotten what's important. To him, and the Avengers."

Captain America continues looking at the empty syringe in his hands wondering why the Winter Soldier saved him.

To Be Continued.


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

Beta: Jebest4781 and Chaos-PSD.

OK as I said above, for filler/one-off eps that deal with mind control I'll either skip it or skim through the parts that deal with it. And will now only have it in if it's something the betas still want to have in, or is important to the plot/later on in the show.

Two perfect examples would be the Young Justice TV show and X-Men: Evolution. For YJ I believe that if the JL wasn't mind-controlled to attack Rimbor, then season 2 would not have happened as the Reach wouldn't get interested in Eath and find out about the meta-gene.

And that would have season 3 not happen if no one knew about metagenes and think people just had power because they're off-world/accident due to superpowers being fairly new in YJ, like a year or 2 before the JL formed from what I found out. And for X-Men: Evo. if the teens and Rogue were not mind controlled then, Apocalypse wouldn't have been freed.

Also, Korra won the poll as I had to end it due to not getting any votes for about a week or 2 and I'm focusing on this story to finish it out due to getting in the last 6 Eps.

Nothing else to say.

Talk To You Later,

Lone Wolf Out.