You are in a theater group and steal a magical princess. Yada Yada Yada, you find out your twin brother is using magic life mist to build an army of dolls... Yada Yada yada, the princess turns a castle into a giant robot to fight the doll army... Yada Yada yada, you go to your alien space ship to find all of your other clones, yada yada yada your clone brother kills you and the only way to realive is to kill Necron the god of death and then the game ends.

Final Fantasy 9, the pinnacle of FF games doing this.

Another favorite for me though would be Breath of Fire.

You are a man, you become a dragon man, you find out you were always a dragon, find the goddess and have to chose between killing her or becoming a dragon god and killing your friends.

Loop hero has you trying to rebuild a forgotten world as you traverse round a simple loop...

mass effect. Shepard kills many reapers, which are pretty close to eldritch gods in another setting.

The entirety of Final Fantasy 14

Most of the Dark Souls are like that, ain't they? I'm too weak sauce to ever reach those levels, though. Black Myth Wukong has you starting Heaven's entire army, so I guess that qualifies too (I'm assuming you end up fighting a god at the end, but again, I'm not worthy)

Final Fantasy Legend, on the Game Boy. There are multiple worlds, and in every world there's a giant tower, and when you enter the tower, each level leads to a different world. Eventually you get to the very top and you fight God, who is guarding the door at the top level that leads to paradise.

Mario and friends find a secret door while on their quest to defeat weapon invaders from another dimension.

Silent Hill and Silent Hill 3 - both games revolve around a cult that is trying to bring about the rebirth of their deity. You play as someone who finds themselves in the town of Silent Hill in search of a person. You solve puzzles, battle monsters, and navigate the town… and then it ends with you fighting a god.

OG Chrono Trigger

Yakuza 0 goes through all the emotions with its storytelling: you start by singing karaoke, then become a fugitive, you go bowling, lose a friend, watch a dirty video...

Also, holy shit, most of you guys missed the point. Edit: Wait, did I miss the point? I thought this post was about wrong games for funsies

Though you DO actually fight a god in Yakuza 5 as a sidequest.

Basically this

Grim Dawn.

One moment you're dying on the gallows, the next you're fighting the tongue of a long dead god trying to reclaim it's appropriated flesh.

And the stakes only get higher from there for the DLCs.