Do not be afraid of cliches. They are cliches for a reason. often they're the better story ideas that fall out from whatever concept they are part of. So one solution would be to simply embrace the cliches and run them ragged. Basically to get them out of your system.
Having done that, the real work can begin. This involves looking at each cliched element in your story and subject them to six tests. The six tests are: why, what, how, who, when, and where.
What are your human subject's super-powers? Who is or was your human subject? How did your human subject use their super-powers? Why is the superhuman being held? Why are they mind controlled? Why are they subject to excruciating torture? Who are the torturers? Why are they doing it? When is this happening? In the past? In the present? In the future? Where? USA? UK? EU? Brazil? Iceland? Cambodia? In an alternative world?
Each question you ask should have a concrete and specific answer. Cliches are cliches because writers reproduce them without asking how or why they work. Putting flesh on the bones of a cliche will bring it to life. Making something that lives and breathes, and has its own autonomy.
Goodbye to Mr Cliche, Say hello to newly minted version of an old story (but only if you look closely enough).