Took on Inspiration from Maximus_Reborn’s Spiders and Magic Story along with Masterrob's basic main conflict which is pretty fucking good, make sure to go check them out on Fimfiction.net!

Equestria

Five Years Later

After the imprisonment of Clayde Reynolds, many ponies in Equestria were worried about the possibility that more humans could enter through the portal but Princess Celestia assured them that there is nothing to worry about. As the months passed, Discord escaped his prison and started reeking havoc on Equestria and started it out with a dragon attacking Ponyville.

In a panicked state, Twilight Sparkle summoned the greatest hero in the universe which happened to be Peter Parker/Spider-Man from Earth 616. He managed to save Ponyville and eventually spent the next six months in Equestria preparing for Discord’s master plan.

Eventually, he fell in love with Twilight Sparkle and he along with her, Princess Luna and Spike went back to Earth and stopped the Green Goblin and the rest of the Sinister Six. After a long battle, Peter managed to defeat Norman Osborn and returned to Equestria but not before Discord revealed his future plans to wreak havoc on Equestria in more worst ways.

The success of Peter Parker allowed Princess Celestia to create a portal to Earth 616 and more Marvel Heroes came to Equestria as their relationships with the heroes of Earth fluctuated greatly.

As time progressed, Peter and Twilight Sparkle had two foals and got married while the many other Avengers got used to the new world.

Now, Peter and Twilight were in their Treehouse Home along with the rest of the Mane Six as they awaited Princess Celestia and Princess Luna. Over the course of five years, the rest of the Mane Five didn’t get along with anyone considering they all had someone else in mind but he disappeared long ago.

“A pretty long wait, not gonna lie.” Peter commented.

“Peter, we talked about this.” Twilight chided softly while giving her husband a soft glare.

“I know its just… a long wait.” Peter replied wistfully as Rarity sighed.

“Darling, please.” Rarity sighed out.

Aunt May trotted into the room with little Ben in her hands as she joined her nephew in the center of the room. She gave a warm smile to everypony in the room before looking at Peter and Twilight.

“Even though the wait is long, it all depends on the occasion.” Aunt May said as Ben wiggled in her arms.

“True.” Peter replied thoughtfully.

“Well Trixie believes it is important considering the fact that Spike ran down here pretty fast the letter.” Trixie commented.

“Whatever the case may be, we just gon have to wait til the Princesses get here.” Applejack said as she tipped her hat.

As if on cue, a bright flash enveloped the area and revealed Princess Celestia followed by Princess Luna, Captain America and Iron Man. The ponies in the room bowed to their benevolent ruler as the Princess greeted them politely.

“Greetings everypony, I hope everything is well?” Princess Celestia greeted warmly.

“As well as ever, Princess.” Peter replied with a chuckle.

“Well then let’s hope it stays that way because I have came up with a solution to keep it that way.” Tony Stark said with a smile as Steve Rogers looked at him unsure with this idea.

“I still don’t think it is a good idea.” He said as he narrowed his eyes.

“Its for the sake of our nation Rogers.” Princess Luna assured him.

“What exactly are you talking about?” Twilight asked curiously.

“Tony, please explain.” Princess Celestia requested.

“So I came up with an idea so that every superhero person or pony can go by without causing a major catastrophe. I made the Accords which will allow superheroes to do legal hero work and only go on missions that we assign to them.” Tony explained.

“The problem with that is that it is limiting one’s freedom to do the right thing.” Steve argued.

“Nooooo, it allows them to keep doing what they do without being penalized or jailed for it, this can help minimize the amount of damage that happens in Equestria.” Tony replied.

“So you’re saying if we sign these Accords, we can do hero work freely?” Peter asked

“Specific requirements, kid.” Tony replied.

“As if we haven’t been doing that for the past five years?” Peter noted as he looked at Tony confused.

“I know it may seem unfair but this provides an opportunity for even ponies to join the Elite Unit.”

“So I can join?” Rainbow Dash asked curiously as she flew up in the air.

“Yes if you abide by the requirements.” Tony replied.

“Aw yeah! I like this idea!” Rainbow Dash cheered as she flew around excitingly.

“So we have to sign these here Accords?” Applejack clarified.

“You are The Elements of Harmony, with you all signed up, it will convince others that the Accords are worth trying out.” Tony nodded to the cowpony.

“It may seem out of nowhere but I encourage you all to give this a try.” Princess Luna pleaded with them as she got nods from everypony which made her smile.

“So what do we have to do?” Trixie asked.

“We will invite everyone to Canterlot and we will make the announcement there so we can make this official.” Tony commented.

“Oh we’re going back to Canterlot! I can’t wait to head back and show off my designs!” Rarity said excitingly as her eyes sparkled.

Everypony rolled their eyes or chuckled at Rarity’s behaviour while Princess Celestia just gave a warm smile at the group.

“Well we better get going, allow me to teleport you all there.” Princess Celestia said as she received nods in confirmation.

Her horn glowed as the Mane Six, Peter, Tony, Steve and Princess Luna returned to the throne room and Tony clapped his hands eagerly.

“Let’s get started then, shall we?” Tony said in a excited tone.

“If it’s in order to protect Equestria than I’m in.” Peter said in a resolved tone as Rainbow Dash flew right beside him with a determined look on her face.

“Don’t count me out!” She said.

“ME TOO!” Pinkie Pie yelled, appearing out of nowhere between the two of them.

“I will happily sign as well, darling.” Rarity said as she elegantly flipped her mane.

“Well shucks, ah’m in too.” Applejack added with an honest smile.

“I-I will join too.” Fluttershy shyly added.

“Me too.” Twilight added with a smile.

“Tony, you have to reconsider this, maybe even make adjustments to this.” Steve pleaded as Tony shook his head.

“Steve please, this is the only way.”

He walked off with Peter, the Mane Six, Princess Luna and reluctantly Steve as they closed the door behind them, leaving Princess Celestia in the throne room alone as she sighed sadly and looked at the setting sun.

“Hopefully this is for the best.” Princess Celestia said solemnly.

Two Hours Later

Soon all the Marvel Heroes and ponies from all around Equestria arrived at Canterlot as they gathered before the castle as they awaited to hear what Princess Celestia has to say. Princess Luna raised the moon as it glowed in the sky and the stars shined bright in the sky.

Soon after this was done, Princess Celestia walked to the podium and the crowd quieted down as they devoted their attention to her.

“My little ponies, I am proud of these past five years as we united with our friends from Earth and were able to keep Equestria safe for awhile, now we are looking forward to taking the next big step… Tony, if you will.” Princess Celestia gestured to her friend.

She stepped aside and Tony Stark took to the podium as he cleared his throat and spoke through the microphone.

“Thank you Princess Celestia, as many of you realized, enemies have been popping up and out of nowhere and when we engaged them, it causes a mass amount of destruction that we have pour resources into and fix. Now I have came up with a potential solution that will require all of you cooperate with it, The Accords are designed for any hero to do legal work and are able to engage villains on my command.” Tony explained.

There was silence in the crowd before one hero broke the silence and this was Wolverine, one of the X-Men.

“Wait so ya want us to give up our freedom just to be commanded, bub?!” Wolverine yelled out in anger.

“No, I will be assigning certain heroes to certain places in Equestria to patrol and keep the area safe. Tony replied calmly.

“Doesn’t sound very safe, what if we don’t sign it and still do hero work?” Human Torch asked.

“Then you will face dire consequences, for a long time we operated on this world without rules, we need to change that.” Tony replied seriously as the anthromorphic ponies looked at each other in worry.

“What about us ponies?” A civilian asked.

“You all can join The Accords and be apart of the hero faction, you will be able to train to eventually join the Avengers.” Tony spoke clearly.

“Sweet!” Thunderlane said excitingly.

“Interesting.” Spitfire commented.

“Wait, if we are entitling humans to protect us, than why aren’t we seeing them as a potential threat to us? Wasn’t that why you killed Clayde?!” Tempest Shadow yelled in anger as she glared at the Princesses.

She shouted this with anger as she was one of the ponies who advocated for Clayde and fought for him but she eventually lost and was in a ticking time bomb state.

The crowd went silent as the human heroes looked around in confusion as Tony also confused along with Steve but the ponies knew exactly what she was talking about.

“This is different, he was a real threat to us!” A random pony shouted.

“But then again he didn’t really do anything.” Another replied thoughtfully.

The crowd began arguing with each other as it soon erupted into violence which forced the heroes to swoop in and break up the fighting as Tony tried to get them to calm down.

“Everyone… wait, everypony please, calm down!” Tony yelled to calm them but it did nothing.

It fell on deaf ears as everypony kept fighting with one another as Tony turned to Princess Celestia.

“Uh, who is this Clayde person their talking about?” Tony asked confusingly.

The alicorn said nothing as she dipped her head down as a lone tear fell out of her eye which did not go unnoticed by Steve nor Tony. The Mane Six were a mixed reaction as Fluttershy, Pinkie Pie and Rarity struggled to hold their tears, Applejack and Rainbow Dash were mutual but they shook their heads sadly while Twilight Sparkle wasn’t really worried at all.

Princess Luna, on the other hand, had no visible reaction as she was the one who punished Clayde for his actions but deep down, she felt guilt and regret for her actions but that was buried away five years ago.

“Is everything okay?” Peter asked in concern

“Y-yes….it’s fine.” Princess Celestia stuttered as she wiped her tears away.

Steve turned to the crowd who were spiraling out of control as the heroes tried to calm everypony down as he gazed at the crowd and narrowed his eyes.

“I don’t think this ‘Clayde’ is a small problem considering the fact that everypony is fighting one another.” Steve noted.

“Maybe this will help…..EVERYPONY, CALM DOWN NOW!!!” Princess Luna shouted as lightning flashed in the sky and her eyes glowed white in anger.

The fighting ceased immediately as everypony looked at Princess Luna in fear as the heroes and the ponies stopped what they were doing and looked at the podium.

“Tony, please continue.” Princess Luna spoke calmly but in a stern tone.

“Thanks, now as I was saying, I don’t know about this Clayde person but we can assure you that we will not become a threat to all of you.” Tony continued his speech.

Half the crowd agreed with the idea but the other half didn’t as they didn’t trust these Accords, especially if it was proposed by Tony Stark.

“So, who’s gonna sign?” Tony asked.

Deep in the Mountains

In the Mountain Ranges, many miles away from the Crystal Empire which is ruled by Princess Cadence and Shining Armor, in a deep, dark cave resides the frozen rock statue of a human with his mouth open in shock as he was in a standing position. Ice coated his limbs as it signified how long he’s been there.

Clayde Reynolds has been imprisoned for five years and it wasn’t the most pleasant way to be imprisoned at all as he stood there collecting ice and dust. Little did he know, he will be freed and return to world more powerful than ever.

Author's Note

WELP, A SECOND STORY THAT IS MOST LIKELY GOING TO GET BOMBED WITH DISLIKES JUST BECAUSE IT AIN'T PERFECT BUT HOPEFULLY THAT'S NOT THE CASE.
THE SAME HAPPENED TO MY BLACK ADAM STORY BEFORE THE RATIO CHANGED TO MORE GREEN THAN RED SO I AM EXPECTING PEOPLE TO DISLIKE THE SHIT OUT OF THIS JUST BECAUSE THEY CAN'T MAKE SOMETHING BETTER THEMSELVES.
This is just me blowing my thoughts out here, be on the lookout for future chapters