Disclaimer: I do not own the Ultimate Spider-Man™ series, Ultimate Spider-Man™ is a sole trademark of Marvel Animation Studios.

Author's Note: This story is pure fiction, and the Phantom is not an actual superhero within the Marvel universe, he is a character I created to make an interesting storyline within the Ultimate Spider-Man series. It's a spread out story that takes place shortly after the last episode in Season 2 of the cartoon series. Phantom himself will take the role of a special character in the history behind S.H.I.E.L.D. and in my opinion; the story will solidify every right for Spider-Man to consider joining the Avengers, even after the events in "Ultimate". Comments and reviews are appreciated, and I will be updating the story as it goes along. Thank you and enjoy :)

Chapter 1: A Special Assignment

Spider-Man swings through the city of Manhattan, shooting webs and slinging from building to building on a cool Friday night after school.

Life as Spider-Man? Not as easy as you think. I'm Spider-Man, the web-crawler around these streets of New York. I'm a super awesome superhero, web-slinger, S.H.I.E.L.D. agent, and normal everyday student at Midtown High. I have an impressive team, who has stood for me since the day I met them.

There's Luke Cage, known to us as Powerman, a great big fellow, with indestructible skin and superhuman strength. He's a reasonable guy, who knows when to stand up for the things he feels is right.

There's Danny Rand, also known as Iron Fist, proclaimed King of K'un-L'un, and wields the Iron Fist, a powerful concentration of his chi. He's an expert martial artist and a philosophical friend, who gives fortune cookie advice.

Sam Alexander, Nova, the bucket-head king of cooking and galaxy trekking. Not exactly the coolest guy to be around, but despite his obnoxiousness, he's a great superhero and a loyal friend. But I'd never tell him that, it'd get to his head.

And last, there's Ava Ayala, White Tiger, a great friend, a dedicated student, and a true realist. She won't hesitate to tell you what's on her mind, and although sometimes she takes things for granted, she truly cares for us as a team. She really is—

"Spider-Man, come in." the communicator rung, displaying a dark skinned, bald man with an eye patch.

And that's Nick Fury, director of S.H.I.E.L.D., the Strategic Homeland Intervention, Enforcement, and Logistics Division.

"What is it, Nick? It's Friday and you know us teenagers have to.."

"Never mind that, Spider-Man. Report to the helicarrier as soon as possible! Something has come up, and I'll need the team on this assignment." Fury told him sternly.

"Oh, all right, but you owe me for taking away my Friday night." Spider-Man sighed.

Without a word, Nick Fury hung up the communicator.

Yep, He owes me big time for this.

Shortly after, Spider-Man swung up to the helicarrier, the massive ship flying in the skies over Manhattan, having withstood many battles and one destruction, its existence is both a representation and demonstration of S.H.I.E.L.D.'s power. He swung into one of the doorways on the top deck, and walked through the metallic corridors to head towards the main conference room. Several agents were walking around with documents in their hands, looking busier than normal, and seem to be in a rush.

I wonder what happened this time, Goblin sighting perhaps.

As he entered the conference room, the rest of his team was already sitting down, with Nova pacing around the room.

"I hate waiting for these assignments, especially when it's on a Friday." Nova complained.

"Hey look, it's webhead." Powerman greeted his friend. The others looked at Spider-Man.

"What's going on, team?" Spider-Man asked them, crossing his arms.

"Not too sure, the whole ship seems real busy today, everybody's up to something." Powerman told him, curious while agents were still walking about in the corridors.

"Yeah, and nobody wants to tell us what's going on, not even Coulson." Nova nagged.

"He wouldn't tell us, it's not like we're on a need to know basis." Tiger added.

"I guess we'll find out soon enough." Spider-Man told them confidently.

Suddenly, Director Fury walked through the conference doors, the tall man looked more stern than usual today, but a look of concern dashed across his face.

"Good, you're all here, then it's about time we discussed what we're up against." Fury paced around the room, dimming the lights and directing everyone's attention towards the hologram in the middle of the table.

"Goblin sighting?" Spider-Man blurted out.

"No, something else." Fury displayed a projection of a building in the middle of a jungle-like oasis. The building had S.H.I.E.L.D.'s insignia engraved on the front of it, while most of the facility remained hidden within the thick of the jungle.

"This is one of S.H.I.E.L.D.'s base of operations located deep within the Amazon rainforest, we maintain covert training sessions there while also keeping an archive of information vital to both national security and international diplomacy." Fury explained.

"Why would you build something like that in the middle of the Amazon?" Tiger asked curiously.

"We figured it was too dangerous to build it anywhere else, it's located in a section that's environmentally hidden and physically impossible to access without the right coordinates or directions." Fury responded.

"So what's the problem?" Nova asked, crossing his arms. "Did it fall under attack or something?"

"We don't know. We lost communications with the base less than 24 hours ago, we've sent agents there to investigate but nothing has returned."

"Sounds like something you could send Iron Man or Captain America to investigate for themselves." Spider-Man told him blatantly.

"I don't want to bother them with something that might not even be as major of an issue than it is, I'd like for you all to consider this as a good field exercise." Fury explained to them.

"I feel as though you feel it is more than what we should know." Iron Fist spoke out.

"I agree." Tiger added.

The director looked out at the agents walking by the conference room with documents and folders. He sighed and looked back at the team, who obviously knew something was up.

Bet this is the work of Goblin or the Beetle.

"I'm not sure of what I know, I'd like for you five to investigate the facility first and see what is going on, and try to search for any S.H.I.E.L.D. personnel. I'll make sure your responsibilities here are taken care of while you are off, good luck to you five." And with that, Fury left the conference room.

Well that was short-lived, it seems like he's hiding something, but that just means we better be careful of who or what we might encounter in the Amazon.

"Look on the bright side guys; at least we get to visit the AMAZON!" Nova cheered on.

"Amusing, I've never been that far into South America." Iron Fist agreed.

"Guys, this isn't a vacation, I'm genuinely concerned as to what we might find down there." Tiger told the group.

"Come on Tiger, we can't give up on an opportunity either." Powerman agreed with the others. "Spidey, what do you think?"

"I'm with Tiger on this one guys, I think we should be careful when we head down there, it doesn't sound too good." Spider-Man told them.

"Alright, we'll play it safe, but I'm telling you webs, it's probably nothing. Fury over exaggerates everything." Nova told Spider-Man confidently.

Although that may be true, it still doesn't explain why Fury was acting so weird about it.

They embarked off the helicarrier onboard one of their aircraft, and set the craft on auto-pilot en-route to the secret base in the Amazon.