Pretty much every page before the weird graphics effects (20, 26, 38, etc.) the MC gives some kind of command, then it takes effects. Some of the commands at the end of sequences (38) are to undo the mind control temporarily. There's a few other spots too, but it's mostly dialog (like having her switch to calling him "Nii-sama" briefly then undoing it back to "Oniichan" when he's testing it out.)
There's also a twist at the end (280-end) where the MC learns that his younger sister has been using it on him for much of the time, that NTR'ing her from her boyfriend has been her idea.