Here is the scene where the Villains finally controls the Indominus Rex in War of the Apocalypse.
(They fired nets on the hybrid)
Tirek: Now it's my turn! (throws some control chips on the Indominus Rex)
(The hybrid dinosaur begins to roar in pain and then it's eyes glow red)
Shredder: Did it work? I demand proof.
Tirek: It did.
(Indominus Rex slowly walk towards the Villains)
Galvatron: It's perfect.
(meanwhile, Bowser was sitting in his throne room with the Dark Staff)
Bowser:(projects himself to Sanctuary to speak with the Other)
The Other: The Chitauri grow restless.
Bowser:(in Loki's voice) Let them grow restless. I will lead them in the glorious battle.
The Other: Battle? Against the the meeker might of Earth?
Bowser: Glorious, not lengthy. If your force is as formidable as you claim.
The Other:(offended and angered) You question us? You question him? He who put the Dark Staff in your hand? Who gave you ancient knowledge and new purpose? When you were cast out, defeated!
(we see the stairs leading to Thanos' throne)
Bowser: I was a king! The rightful king of the Mushroom Kingdom. Betrayed.
The Other: Your ambition is little and full of childish need. We're beyond the Earth to greater worlds. The Yellow Chaos Emerald will avail.
Bowser: You don't have the Yellow Chaos Emerald.
The Other:(moves towards him)
Bowser: It wasn't a threat. Just a reminder. But until I open the doors, until your force is mine to command, your claims are nothing more than words.
The Other:(moves around him) You will have your war, Koopa. If you fail, if the Yellow Chaos Emerald is kept from us, there will be no realm, no barren moon, no crevasse where he cannot find you. You think you know pain? He will make you long for something as sweet as pain.(touches the side of his face, forcing Bowser to pull out)