Here is how Indominus captures Frost and Ursula, Indominus unlocks her true potential, and Nighlock is free goes in Pooh's Adventures of The Myth of Burton.
(we see Emma Frost and Ursula telling the prisoners how the world will soon be their's)
Emma Frost: Soon, mutantkind will rule the world.
Ursula: And there is nothing you can do to stop us!(laughs)
(we see Indominus hiding in the shadows waiting to make her move)
Emma Frost: So you can either join us today.
Ursula: Or you can stand against us.
Indominus Rex:(from behind them) Or the two of you wake up in prison tomorrow.(steps out of the shadows, and unsheathed her claws)
Emma Frost: Indominus don't do this. You were never cut out to be a hero.
Ursula: You are freak of nature. The humans will never accept you.
Indominus Rex:(in Captain America's voice) That's not the way I see it.
Indominus Rex:(in Adagio Dazzle's voice) Let's battle.(eyes turn into their natural color, and she attack viciously)
(Frost can't shut her down because the red eyes block her out and Ursula can't grab her because she is too flexible)
Indominus Rex:(slams Frost on the ground)Thought you people were strong.(ties up Ursula)Well you're not strong enough.
(she drags them to Nighlock's cell and begins trying to cut the chains)
Nighlock: It's no use, save them without me.
Indominus Rex: I was taught, never leave an agent behind, and I won't. I'm breaking this chain even if it takes me years.(glows silver and cuts the chains) There you see. I ain't leaving a friend behind.
Nighlock:(puts Frost in chains with Ursula) Let's go save the X-Men and Brotherhood.