I placed the ender crystals down to respawn the dragon, I didn't feel like fighting the dragon that day, so I left while they were doing their thing.

Came back into the game the next day and crystals were doing nothing, they were just in that weird formation.

The portal to the overworld was gone, so I was stuck there.

I've tried exiting the game and coming back, going into an end gateway, nothing seemed to be working.