Our idea of the atom has changed a lot over the last hundred years or so, because every new experiment showed that the old picture was wrong somewhere. Here are four of the biggest steps.
Intermediate mode:
In standard mode every question tells you the number of electrons, and the ions are simple, common ones. In intermediate mode the electron count is left out, so you need to know each element’s protons yourself, and the ions can come from almost any element. Switching modes restarts the game.