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)