After the team left the bridge they started to go to the launch bay to stop the missiles. As they where running through the Helicarrier 2 of Ultron's robots locked the door and destroyed the Energy Converter for the room that they where in.

y/n: Without that converter we're stuck in this room. We need to find a new one!

After they destroyed the robots, they search the room until Spider-Man found a new one.

Spider-Man: Hey guys! I found an Energy Converter!

Captain America: Nice work Spider-Man. Thor can you put the converter in place? Sonic Shatter and I will remove the old one.

Thor: Of course captain.

y/n and Captain America worked together to remove the broken converter while Thor put in the new one, then the console turned back on and Spider-Man used it to open the door.

y/n: Nice! Now lets go. 

After running through the ship and fighting some robots the team arrived at the launched bay.

Wolverine: Alright Fury we're at the launch bay. How do we stop the missiles from launching?

Fury: You'll need to destroy both of the consoles.

Wolverine: Go it!

The team managed to destroy the console on the right but when they destroyed the console on the left, the missile was already launched.

Spider-Man: Uh oh...

Fury: I just got intel saying that one of the missiles was launched. I thaught I told you to destroy both consoles?!

Spider-Man: Give us a break Fury. There wasn't enough time!

Fury: (sigh) Ok, to stop the missile you'll have to activate the self-destruct system for it!

Spider-Man: You got it!

The team then went to the center of the room to stop the missile but when they got there Bullseye stood in their way along with two robots. 

Bullseye: Well well well, looks like we got some heroes here.

y/n: Bullseye! What are you doing here? Get out of our way, we need to use that computer!

Bullseye: You think you're going to shut down the missile I just launched? You can't do that without getting the access card from me.

Captain America: Well then, looks like we'll have to beat you first to get the card.

With that, the heroes battled Bullseye and y/n managed to defeat him by throwing one of his Sonic Bombs at him and Bullseye threw at knife at it. Then they took the access card from the unconscious assassin and used it on the computer to activate the missiles self-destruction system and the missile safely exploded over the city.

Fury: Good job, the missile harmlessly exploded before it could do any damage.

y/n: No problem Fury.

Black Widow: Colonel Fury, the Masters of Evil are attacking our stabilizing engines. There are too many for me to handle alone!

Fury: Black Widow do not engage the enemy. Get out of there immediately. Team I need you to same our engines double time.

y/n: We're on it!

The team then went to the lift  that took them to Black Widow's position but there was a lot of damage there. 

Captain America: Fury we're off the lift but it looks like an explosion happened.

Black Widow: That was my fault I'm afraid, luckily I was not harmed.

Fury: Widow I though I told you not to engage the enemy!?

Black Widow: I am sorry sir, it was unavoidable.

y/n: Don't worry Widow, just stay safe we'll take it from here.

Black Widow: Thank you. And good luck.

The team continued to run through the ship and destroyed more robots but then Spider-Man noticed a damaged laptop on the ground.

Spider-Man: Hey guys! Check out this laptop.

y/n: That must be Widow's laptop, we should return it when we're done.

Spider-Man: Or, we could keep it and see if she's hiding any thing.

Thor: It is strange how she disobeyed Fury's orders.

y/n: She said it was unavoidable! But if you want to risk her finding out you're going through her things then fine.

They continued to fight through the ship, then they came across some locked room with agents inside.

Agent: Hey! Thank God you guys are here, someone named the Winter Soldier came in and locked us in with our own security.

Captain America: Don't worry we'll get you out. Where do we go to shut them down?

Agent: The console for these fields are in that room (points to the room beside him) but be care for, the Winter Soldier has likely placed laser trip wires there. If you trigged them a bomb will go off.

Captain America: Thanks for the intel. We'll be careful

The team then entered the room when y/n noticed the laser.

y/n: Hold on a minute. (He threw on of his sonic grenades and destroyed the bombs) That should do it.

They then used the consoles to shut down the security system and set the agents free.

Agent: Thanks for the help, it was a little embarrassing being trapped by our own security system.

y/n: No problem, but you should get to the bridge to help Fury.

The agents nodded and ran off, and the heroes continues their mission to same the engine. They kept fighting until they found 2 more supervillains, The Winter Soldier and Radioactive Man.

Captain America: Winter Soldier, give up, I'm here to stop you!

Winter Soldier: Captain America, can't say it's good to see you.

Thor: Radioactive Man, surrender I will not let you destroy the engine.

Radioactive Man: Thor, it is a pleasant surprise to see you too.

Captain America: Listen to me, if you destroy those engines the this ship will crash and thousands of lives will be lost!

Winter Soldier: No can do, I got my orders. You understand right Cap? Orders where always so important to you.

Thor: We don't have time for your blabber, surrender or suffer my wrath.

Radioactive Man: If it is a fight that you want then it is a fight that you'll get.

With that the heroes and villains fought but in the middle of the fight Dr. Doom contacted the villains.

Dr. Doom: Winter Soldier, why haven't you destroyed the stabilizing engines yet.

Winter Soldier: Sorry, we got carried away but we are on on it!

Radioactive Man: It is lucky for you we must depart, I was just warming up.

Wolverine: Hey! Where do you think you're going!

The heroes followed the villains.

Winter Soldier: See! I told you that they would follow us. They're as predictable as the sun rise.

Radioactive Man: The come heroes, follow us some more.

The villain ran off. 

Spider-Man: My Spidey sense in going of, I have a bad feeling about this.

Wolverine: Whatever, the bad guys are getting away (He accidentally activated a lased trip wire and an explosion occurred) UGH!

y/n: (went to check on Logan) Are you ok?

Wolverine: Yeah, I'm good. (looks around) But where did they go?

Winter Soldier: Looking for someone?

The villains when on the upper level.

Radioactive Man: Now lets see hoe you handle this force!

With that the villains left and a group of robots entered the room.

y/n: I got this!

Sonic Shatter took out his sonic cannon and shot it at the robots destroying them all at once.

Captain America: Nice work, now lets get after those villains!

The heroes managed the find the villains.

Radioactive Man: You're too late. In a few moments the Winter Soldier will activate this cannon and we will fire it into the engine.

Wolverine: We aint let'n you do that bub!

Winter Soldier: Don't you understand! You can't stop the Masters of Evil, we're just too powerful, abandon ship while you still can.

Radioactive Man: It does not matter, they will not live long enough to stop us.

Winter Soldier: Lets make sure of that shall we?

The heroes and villains once again fought but this time the heroes won. The Fury called them.

Fury: Well done! I wish there was time to rest but we've got big trouble on our hands.

y/n: What trouble are you talking about Fury?

Fury: The Masters of Evil have unleashed some kind of creature, I need you guys to take it down. Get to the lift asap.

y/n: We're on our way.

The team then went to the lift and found themselves on the torrent station. Then the creature landed in front of them, its was Fin Fang Foom!

F.F.F: Puny humans, you are foolish to challenge the might of Fin Fang Foom!

Thor: Give up vile creature, the Masters of Evil have lost.

F.F.F: It is you who have lost once I send this ship crashing into the ground, then the world will see that the Masters of Evil are a force to be recon with.

Wolverine: That aint going to happen bub!

F.F.F: As if you have any saying in the matter mortal.

The heroes fought hard against Fin Fang Foom, and when he flew off they had to use one of the torrents to hurt him but eventually they defeated Foom and the Helicarrier was safe.

Fury: That wasn't the most graceful battle I've ever seen but you saved the Helicarrier. Thanks Team.

Captain America: Our pleasure sir.

Fury: When you're done there return to the bridge, we're moving to Stark Tower for our next mission.

y/n: Next mission? What are you talking about?

Fury: Come back to the bridge and you'll find out. And y/n, try not to keep you girlfriends waiting.

y/n blushed and they all went back to the bridge.