Avoid these story cliches:
- the mysterious protagonist is actually an alien, robot, AI, elf, ghost, monster, insert_your_favorite_creature_here
and closely related: the seemingly normal protagonist is actually an evil murderer/torturer
- the mysterious seemingly-not-human protagonist is actually a human
and the closely-related: mysterious planet is actually Earth
- nonhumans act exactly the same as humans.
- the protagonist discovers he/she/it is the special chosen one
- brave knight saving the damsel in distress and/or killing the dragon/beast
- the powerful magic-object/wizard/AI/etc. saves the day
- scientists/science are/is evil
Subverting cliches, on the other hand, can work great...
Good luck avoiding cliches!