A good clicker game with a story is 'Realm Grinder'. It has a complex story where you choose between different factions, like angels and demons, and your actions impact the world. You click to generate resources and use them to build your realm. 'Idle Apocalypse' is interesting too. Here, you are an evil overlord and you click to summon minions, expand your tower of doom, and the story follows your journey of world domination. There's also 'Nuclear Throne' which is a post - apocalyptic clicker game. You click to fight mutants and other threats in a world gone mad, and the story is based on survival in this harsh environment.
A great clicker game with a story is 'Clicker Heroes'. The story is about ascending heroes and fighting through various levels of monsters. You click to attack the enemies and earn gold to hire and upgrade heroes. It has an interesting progression system that ties into the overall story. 'Ninja Kiwi's Bloons TD Battles' also has a clicker aspect. The story involves defending your base against waves of balloons. You click to place towers and upgrade them to fend off the attacks. Each level and tower upgrade is part of the strategic story of protecting your territory.