Here is how Attack on the Manehatten base/Shadowcat, War Machine, and Bishop get captured by the Pro-Reg, Vision, Scarlet Witch, Apocalypse, and Quicksilver arrive, and Sunset, Luna and Human Torch get captured by the Anti-Reg goes in Equestria Civil War.
(we see Peter in his Spider-Man costume running from a Canterlot chopper)
Royal Guard:(into Comm) Unregistered minor tried to foil a robbery in costume, Air-Command. Identified as Codename: Spider-Man from the Avengers. Am currently in pursuit.
Air-Command Pony:(on Comm) Roger that, Foxtrot Four. Permission to use tranquilizers and minimum force.
(the choppers fire at Peter, but his suit resists the shots)
Royal Guard: This little punk's suit is bulletproof now?
Royal Guard #2: Darn info-base. I thought we had ponies updating this thing.
Spider-Man:(jumps into a building, the glass cutting his costume)(yells)(into Comm as the helicopts appears) Guys, we gotta get out of here! Canterlot Forces just caught me breaking up a mugging, and now they're all over me! This is serious! Nighlock was kidding when he said these ponies are not kidding around when they say they don't want anyone solving their problems for them!
(the chopper fires a gass grenade into the room)
Spider-Man:(shocked) Oh, boy--
(the gass explodes, destroying the top of the building)
(some guards who have just captured Bruce, Clint, Scott, Wanda, and Vision, along with Peter)
Royal Guard #1: You sure that kid's indestructible?
Royal Guard #2: He'll be fine. It's the office block I'm worried about, dude. Command said property damage gotta be kept to a minimum or it's head rolling time.
(he turns to the captured heroes)
Royal Guard #2:(to the captured Avengers) You see the trouble you caused? You see what happens when you try to be some big bad vigilante like your buddy, the Princess of Friendship?
("Elsewhere" appears on the screen)
(we see Piotr and Steve at a computer)
Captain America: Canterlot unit just picked up some of the Avengers on West 23rd. Should we get a posse together and intercept?
Colossus: Twi and Rainbow are already undercover on the scene, Captain. Funny Rainbow Dash even told me to get the darn coffee on.
[cut back to the convoy]
[we see a Royal Guard in the shotgun seat and Twilight, in disguise, in the driver's seat]
Royal Guard: Se, this is what I'm talking about: these people are what, in their 30s? 40s tops? And they're out there in their pantyhose laughing in our faces, about the Accords.
[Twilight doesn't respond and clearly has no interest in this conversation]
Royal Guard: It's not like we're banning 'em, man. Nobody's stopping 'em doing their thing. Heck, they're even paying these clowns to go official now.
[Twilight still doesn't say anything]
Royal Guard: But they don't get a buzz outta bein' legit. Freaks only get off on the villainy and mystery pony garbage.
[Twilight doesn't say anything]
Royal Guard: Gonna be one cold shower they get when they see the new pen they're building for these reformed creeps. You heard about this place? This "Number 45" thing they're constructin'?
[Twilight doesn't answer]
Royal Guard: Fino in supplies said you're not even allowed to look at the blueprints without these weird eyed special goggles.
[Twilight finally looks at him]
Twilight Sparkle: You know something, fella?(fires a magic blast, knocking him out of the vehicle) You talk too much!
(the guard screams as police cars swerve to avoid him)
Royal Guard: SON OF A--!
(the police cars crash)
(inside the vehicle)
Rainbow Dash:(removes Wanda's power dampers) Scarlet Witch, I need you to rustle up one of your teleportation spells and I need it now. Understand?
Scarlet Witch: Y-yes, ma'am.
(cut back to outside as police block the road and a chopper follows)
Chopper Pilot Pony: Attention all units in the George Washingtrot Bridge area! Suspected hijacking of Canterlot Bus 1! Please attend! I repeat: Please attend!
(cut to the driver's seat in the vehicle)
Twilight Sparkle: Cops and Royal Guards are blocking the road already, Rainbow Dash!
(cut to the back of the vehicle)
Rainbow Dash:(inpatient)(to Wanda) Would you hurry up that fraggin' spell?
Scarlet Witch:(in an unknown language)(translates to: "I want to be somewhere else. I want to be somewhere else...")
(cut back to outside, the cops and Royal Guards have the vehicle cornered)
(but we can see scarlet circles in front of the vehicle, signifying the spell is working)
Royal Guard Pilot:(over radio) Lunatics are gonna kill themselves! Block the road and stand well back!
Police Pony:(over radio) Roger that, air-support!
(we now see the spell going into full power as the vehicle is about to crash into the barricades)
Scarlet Witch:(offscreen)(in an unknown language)(translates to: "I want to be somewhere else. I want to be somewhere else...")
(the spell works and the vehicle disappears into thin air)
(it later reappears in an abandoned warehouse)
(the door to the prisoner hold opens)
Ant-Man:(steps out first with Clint) Oh, God. What's happening? Where are we?
(the people present are Captain America, Dr. Whooves, Nurse Redheart, Thor, Colossus, Nighlock, War Machine, and Shadowcat)
Nighlock: Congratulations, friends. You just joined the Equestrian Resistance.
(Twilight and Steve start helping them out of their cuffs)
Ant-Man: What... what is this place?
Twilight Sparkle: Canterlot Safe House #23. One of 28 such places peppering Equis and only known to 33 Degree Canterlot Officers.
Bruce Banner: And how many of them are there exactly?
Twilight Sparkle: Just Thaddeus Ross.
Captain America: He's back on Earth, and underground now too. And can only be contacted via scambler-phone, but he said we could use this place for as long as we like. And he's already working on our new secret I.D.s should we lose this war.
Spider-Man: Why do we need new secret identities?
Nighlock: Your old ones are probably compromised, Spider-Man, and you're going to need somewhere to hide when we aren't out there kicking butts and taking names.
Twilight Sparkle:(removes her fake glasses) This is where we live for the duration. Moon Dancer's crew is planning something huge out there, and this is where we start to fight back.
Shadowcat:(notices something on the TV)(points to it and turns to the others) Guys, I think you better see this...
(and on the screen was Moon Dancer speaking to the public)
Nighlock:(into his comm device) Nighlock to all units. Wherever your are, turn your TV on now.
(cut to Waterfall D.C.)
Moon Dancer: Fillies and gentlecolts, ladies and gentlemen, I'm sure I don't have to introduce you to Misako. Misako, you may recall, lost her brother in the Ponyville Town Hall Incident and helped kick-start my passion for the federal employment of all reformed villains.
(cut to Scott Summers, Jean, Hank, and Juggernaut watching the news in Canterlot Safe House 13)
Wolverine:(walks in) Heck's going on now?
(cut back to Waterfall D.C.)
Moon Dancer:(gestures at a landing Mare Do Well) Likewise, I'm pretty sure Mare Do Well needs no introduction.
(cut to Sonata visiting El Diablo in the hospital)
Sonata Dusk: I hope you know what you're doing here, Moon Dancer...
(cut back to D.C.)
Mare Do Well: Um, as most of you know, I've uh, guarded my secret identity pretty carefully over the years... And it's only after a long talk with my parents and my sisters that I've decided to take the following step.
(cut to KC, Morro, Motor Man, and Harley watch this on TV)
Mare Do Well:(on TV) See, the Accords give us a choise: We can continue the trend that the Princess of Friendship advocates and have poeple and ponies who used to be villains completely unchecked...
(cut to the Pie Family watching this as well)
Mare Do Well:(on TV) ...Or reformed villains can go legitimate and earn back a little public trust.
(cut to Lionheart's office, as he watches in horror with some of his staff)
New Assistant Mayor: Mayor Lionheart?
Mayor Lionheart:(holds up his hand to silence her) Ma'am, you even think about asking me what I want for breakfast and you're fired, little lady.
(cut back to D.C.)
Mare Do Well:(starts removing her mask) I'm not wearing my old mask because I'm ashamed of who I am, and I'm here right now to prove it...(removes her mask, revealing she is Pinkie) My name is Pinkie Pie, and I've been Mare Do Well since I was the Element of Laughter.
(cut to Lionheart's office as papers fly off the desk, and he is nowhere to be seen, signifying he is having a heartattack)
New Assistant Mayor: Mayor Lionheart?
(cut back to D.C.)
Pinkie Pie: Any questions?
(many reporter ponies try to ask her questions)
Moon Dancer:(puts her hoof around Pinkie's shoulder) Soak it up, Pinkie. You're bigger than Elvis, now.
(cut to a transmission showing the Equestrian Avengers symbol)
Twilight Sparkle:(on transmission) Bad news -- our base in Manehatten has been discovered by Canterlot.
(we see the layout of the base under attack)
Twilight Sparkle:(on transmission) Bishop was in charge of setting this operation up, but we've lost contact with him. We need to recover weapons crucial to our movement, and -- more importantly -- protect the data. Bishop had complied regarding our allies and other prospective base locations. From what we can tell, the base defenses are already compromised. Get there ASAP, and hit those invading Canterlot forces from behind. Then get our people and ponies and our intel out of there.
(the transmission ends)
(we see Canterlot forces attacking the base)
(we see Vision, Wanda, Pietro, and Nur ready for combat)
Bishop:(on Comm) Team, this is Bishop. Canterlot is placing explosives to destroy our combat drones. Take out their soldiers and disable the bombs. I'm dispatching Shadowcat to help you.
(they set off and come across some enemy soldiers)
Royal Guard: Unregistered reformed villains!
Scarlet Witch: Register this!(fires her magic, knocking them aside)
(they go through the door to the outside)
(more soldiers attack them)
(they beat the soldiers)
Shadowcat:(jumps down from a building and lands in front of her allies) Get onto the boat! Canterlot's trying to destroy our equipment!
Quicksilver: When's the last time you were a rebel?
Shadowcat: We don't have much time for that, Pietro!
(they go onto the boat and battle soldiers)
Shadowcat: Grab those explosives and get them away from the cargo!
(they defeat some soldiers and throw off 1 bomb)
Shadowcat: Clock's ticking!
(They throw off another bomb, defeating some more soldiers)
Shadowcat: Remove those bombs!
(they defeat some more soldiers, while Vision throws off the 3rd bomb)
(they defeat some more soldiers and Wanda telekinetically throws off the 4th bomb)
Shadowcat: Get the explosives off the boat!
(they defeat some more guards and Pietro throws off the 5th bomb)
(Nur finishes off the soldiers and throws off the final bomb)
Shadowcat: All of our gear is safe, thanks to you.
Scarlet Witch: Where's Lucas?
Shadowcat: Bishop's holed up nearby, in an old HYDRA base we repurposed.
Scarlet Witch: HYDRA? But how could they have known of this world?
Shadowcat: I'm not sure. We'll have to ask Red Skull that. We've got people and ponies to protect.
(they go over to the gate)
Bishop:(on Comm) I'll get the open. Get in here and stop Canterlot!
(they fight their way through some more soldiers)
(they take down a few helicopters)
(they reach the base and a helicopter is waiting for them)
Bishop:(on Comm) Grab those mines! Use them to hit the chopper!
(they throw the mines at the choppper, and it blows open the entrance)
(they go inside)
(we see Luna and Johnny trying to get in)
Princess Luna:(fires a magic beam at Johnny, charging up his fire)
Human Torch:(fires a super hot fire beam that breaks past the wall that leads into the true base)
(they go in with some soldiers, leaving Sunset behind)
Sunset Shimmer:(faces them) Your stunt in Canterlot was cute, but this is just lunacy.
Quicksilver: I've never been one for following all the orders.
Sunset Shimmer: You're facing down all of Canterlot and taking on our own government. Regardless, I can't let you go further. I don't want to fight you, but you're giving me no choice.(into Comm) Soldiers! Form up here!
(they begin fighting)
(they defeat Sunset)
(two Crystal Ponies hold her by the arms)
Shadowcat:(walks up to her) Did you honestly think we'd be unable to call in reinforcements, Sunset? Your biggest weakness is your overconfidence.
Sunset Shimmer: I could easily say the same thing to you, Kitty. You can't win this war.
Shadowcat: Time will tell.
(the energy field Sunset had put up in front of the entrance deactivates)
Bishop:(on Comm) I've disabled Sunset Shimmer's security override. Get inside, now!
(they go inside)
Bishop:(on Comm) We're mounting a defense just ahead of your position. Move in and hit Canterlot from behind!
(they fight their way through Canterlot guards)
(they then arrive in an area where both sides have been blocked off by force fields)
Time Turner:(on Comm) Bishop, this is Time Turner. Human Torch and Princess Luna got past us before the forcefield went up!
Bishop:(on Comm) Acknowledged, Time Turner. We'll be on the lookout.
(suddenly, guards attack them with big robot mechs that are Hulk size)
Bishop:(on Comm) Meanwhile, hold the line! Those Canterlot Devastators are ripping the base apart. Take them out!
(they battle the soldiers)
(Apocalypse then tears apart the robots)
Bishop:(on Comm) Great, I'll open the passage to the right.
(the force field on the right lowers)
Bishop:(on Comm) The electrical subsystem's overloaded - I need you to turn the turret defenses online.
(they fight their way through more guards as they come up to the control room)
Bishop:(on Comm) You need to get into the control room.
(as soon as they try to, electricity crackles and blocks their entrance)
Bishop:(on Comm) Find someone - or something - who can get through the electrical field.
Apocalypse:(motions for the other three to hold back as he goes up)
(the electricity parts way for him)
Apocalypse:(uses his powers to overload the electrical field, disabling it)
Bishop:(on Comm) Good. Now cycle the power to restore power. You'll have to hit the switches in the right order.
Vision:(hits the switches in the right order)
(we then see the turrets fire upon approaching soldiers and robots)
Bishop:(on Comm) Turrets online! That'll put a few in those bots.
(as they are heading back to the force fields)
Shadowcat:(on Comm) Six Star Forces and Crystal Ponies, this is Shadowcat. Our position is being overrun by Canterlot reinforcements! Watch your backs - unnh!
(her comm shuts off, signifying she has been captured)
Bishop:(on Comm) Kitty?! Darn! Get back to the central hub and stop Canterlot!
(they head back to the force fields)
Bishop:(on Comm) Human Torch's blasting holes in our defenses! Take out those troops!
(they proceed through the next passage and take out the troops)
Bishop:(on Comm): We've got a chance now. Meet up with me in the rear of the base and we'll plan our next move.
(we see Canterlot bots opening doors and holding them up to let more troops in)
Bishop:(on Comm) Hang back, those bots are prying open the doors. I can seal 'em out, but it'll take a moment.
(they then take out the soldiers and destroy the bot)
Bishop:(on Comm) First door secured. I'll work on the other two.
(they destroy the other two bots)
(we then see a part of the wall glowing as it is busted open)
(Luna steps out)
Princess Luna: We'd ask if you're going to come quietly, but thee has that already a few times tonight.
(they start fighting and beat her)
Bishop:(on Comm) She wanted a war: she got one. Now head - Human Torch?! Team, get down here! We've got trouble! Ungh!
Human Torch:(on Comm) Yeah, why don't you come down here? You can wave goodbye to Bishop while we drag his sorry butt to jail. Unless you think you can stop us...?
Bishop:(on backup Comm) Test... test... Team, this is Bishop. I'm in lockdown here, but I can send you burst transmissions via the backup commlink. You need to reach my position and stop Human Torch before he downloads our intel.
(they then go into the lower levels of the building)
Human Torch:(on Comm) As you can see, we've made ourselves at home - hope you don't mind. Support team to the entrance! Stop those unregistered reformed villains!
(they fight their way through many soldiers and find War Machine's shoulder cannon, signifying he had been captured)
(they then see a bot draining power from an electric core)
Bishop:(on backup Comm) That robot's locked into a power terminal. I need you to knock out three of those terminals so I can clear your way hear.
(they destroy the robot and the terminal)
Bishop:(on backup Comm) Good work. I'll point you toward the other two terminals.
(they then head to the next terminal)
Human Torch:(on Comm) They're heading toward the second terminal. Stop them!
(they fight through many soldiers and then destroy the 2nd terminal)
Bishop:(on backup Comm) Another one down... watch it! Movement in the ventilation system. Converging on your position!
(they defeat the smaller bots)
Human Torch:(on Comm) Don't let them take down that third power terminal!
(they arrive at the 3rd power terminal and destroy it)
Bishop:(on backup Comm) That did it. Now - watch it. That bot's fully charged!
(they fight and destroy the bot)
Bishop:(on backup Comm) I can unlock the central command now. But Human Torch's camped here. You'll have to get past him to reach me.
(they enter the central command where Human Torch is waiting for them)
Human Torch: I understand you think you're doing the right thing, but you're not. And I don't have to explain why. Either back off, or suffer the consequences.
Scarlet Witch: Oh, we won't do that.
(They start fighting)
(Eventually he is defeated)
(Then a hologram of Moon Dancer appears)
Moon Dancer:(on hologram) Human Torch, have you -(sees he is down)- ah, dang it. I knew I should've supervised this op personally. Next time, you turncoats won't be so lucky.
Quicksilver: Should've listened to us.
Moon Dancer:(on hologram) If you were smart, you'd stop this foolishness. But I can see you want to play this the hard way. So be it.