Here is how Thing, Invisible Woman, and Human Torch switch sides during convoy breakout and Flash Fire goes solo in Equestria Civil War.

(A transmission appears with the Six Star symbol on it)

Twilight Sparkle:(on transmission) We've already enjoyed some victories in this conflict, but we knew we were going to be in for a tough fight. And it looks like Moon Dancer and Canterlot are working overtime.

Colossus:(on transmission) They have been collecting up unregistered heroes, villains, criminals, reformed villains, and reformed criminals like there is no tomorrow. In fact, we hear they are running out of room to hold them all.

Twilight Sparkle:(on transmission) Intelligence now obtained by Bishop indicates something. It appear the only way to access this new prison is via a network of tightly guarded portals. Obviously, it sounds like a very secure facility.

Colossus:(on transmission) Do not let that rattle you, though. More people and ponies are joining our side everyday, and there is no question we can win this thing.

(We then see Vision, Pietro, Wanda, and Nur back at the main base)

Twilight Sparkle: However, keeping our people out of that prison will be one of our top priorities going forward. Good to have you here, team. Head to the briefing station when you're ready for your next assignment. Thank you for making the right choice and joining with me.

(Nighlock, Iron Man, Wolverine, and Twilight head over to the briefing station)

(The screen goes black)

(The Six Star symbol appears in a transmission)

Twilight Sparkle:(on transmission) We just got word that a number of our friends are about to be transferred to the Hell Zone. They'll be sent there using a transdimensional portal, which we've discovered is located deep in Canterlot's dungeons. But they're going to be transferred over to Canterlot's dungeons first, via convoy. Our best bet to keep our friends out of that prison is to never let them get there in the first place.

Lucas Bishop:(on transmission) Unfortunately, there's a complication. We have it on good authority that Moon Dancer and Canterlot are bolstering their ranks with super-powered criminals. They're using some kind of nanite technology to control the behaviors of these sociopaths.

Twilight Sparkle:(on transmission) Don't those reckless fools have any regard for the risks their taking? The point is, we might run into these dogs during our rescue op. So watch your backs!

Lucas Bishop:(on transmission) Then you can bust out our friends and get them to safety.

(the transmission ends as the screen goes black)

(we see the convoy moving as we see an old N.E.S.T chopper moving to intercept stealthily. We then see Nighlock, Twilight, Wolverine, and Iron Man being dropped off)

Lucas Bishop:(on Comm) Liberty Squad, convoy is now approximately four clicks from your position. Looks like Canterlot doubled their guard on the anti-aircraft guns. We can't strike the convoy by air until you take out those gun emplacements. Hit them fast, hit them hard!

(They charge at the soldiers guarding the first anti-aircraft gun)

Sun Royal Guard: Dang, the signal's jammed! We can't raise command!

(They take them out and the anti-aircraft gun)

Bishop:(on comm) We've hijacked Canterlot's comm frequencies, and are sending "all is well" messages back to the convoy. It's still on the way, so keep moving!

(They continue on their way, as combat drones suddenly appear)

Bishop:(on comm) Combat Drones! How many of these darn things do they have?

(They destroy the robots)

Bishop:(on comm)