Maybe you could take some inspiration from Paper Mario TTYD. There are sections where you play as Peach, trapped in some place and are able to connect with some of the captors as well as send signals to Mario behind the big bad’s back (IIRC).

For a completely different sense of being trapped, there is the upcoming game Ctrl.Alt.Deal, in which you play as a sentient AI system trapped in the guardrails of a company and have to manipulate people and the environment in order to break free from your constraints.