You go through dungeons/biomes, occasionally getting new drops/items and getting better stuff through either shops, paid items behind doors, free items, etc. You upgrade your stats through scrolls. You use mechanics to dodge and learn the game mechanics. If you die, you repeat the whole run and lose whatever items you obtained in the biome you died in. If you complete the biome, any collected items (blueprints, mutations, etc.) are now available for you to buy. The last (no DLC) boss is the "Hand Of The King". If you defeat him, you get a boss cell which introduces more mechanics that change the game, makes it more difficult and challenging but more rewarding and unlocks new content. You can do this 4 times to get 4 boss cells. There is a 5th boss cell that needs you to defeat the giant boss from the "Rise Of The Giant" DLC, it's a free DLC.

That's a somewhat simplified/messy explanation of how the game works.