This is exactly the same as how you used the instruments to wake The Silent One. You could consider taking a screenshot of the Music Score to keep next to you, while watching the Disciples movements.
I need an explicit spoiler.
Have Henry go to his instrument. Click on the teal Disciple. Watch carefully, match the arm and leg positions to the Music Score. Repeat for Mum and the green Disciple. This process will repeat three times, getting incresingly more complex.
I need an explicit visual spoiler.
I'll draw the solution here. I do not know if it will be the same for your game. If not, can you please let me know and I'll remove this. (In fact, I think what I just did was different from last playthrough, so you may be on your own. Good luck.)
Phase 1. Henry first. Then Mum.
Phase 2. Henry first. Then Mum.
Phase 3. Henry first. Then Mum.
Get the Chrono Crystal. It's purple and just below the Beast, on the Altar.
Take the Chrono Crystal back to the Universal Machine.