I keep circling back to this because the whole mutation angle hits differently when it's not just a power-up but an actual identity crisis. 'The Metamorphosis' by Kafka is the obvious classic, but honestly, it's more philosophical horror than a plot device in the modern genre sense. For a plot device, you want something where the mutation drives the story forward, creates new problems, changes relationships.
A recent one that nailed this for me was 'Gideon the Ninth'—though the monster mutation is more of a creeping, necromantic body horror for certain characters. It's not the main lead, but the way their physical forms break down directly alters alliances and reveals secrets. That series treats mutation like a slow-acting poison for some and a twisted ascension for others. The plot can't move without those physical changes.
I also think of 'Annihilation' by Jeff VanderMeer. The whole area is basically a mutation engine, and the biologist's own transformations are the key to unlocking the plot's mysteries. It's less about fighting monsters and more about becoming one to understand. That book ruined normal forests for me, in the best way.
There's a whole subgenre in web serials where the MC starts mutating after a system integration or a mana surge, and their struggle to control it or hide it from society becomes the central tension. 'Chrysalis' on RoyalRoad comes to mind, where the ant protagonist's mutations are literally his progression system.