I have gotten the first half of the rod from the Avatar dude and went to Sassar, he tells me the next plan. But instead of following his plan, I wasn't paying attention to the names and ended talking to Gaal instead of Tad and he then summons The Eyeless One so I ended up killing everyone that wanted a fight. Now I only have one piece of the rod and everyone is missing including Tad Then I read my journal and it saids to go back to the Temple so I went back to the Temple Of Helm and The High Watcher Oisig is missing too. Would anyone know what the hell went wrong?

I've never actually gone down this route, but can't you go back to the beholder warrens and retrieve the second part of the rod, then take it to the cult god to complete the task? Destroying Gaal was always going to happen anyway, right?

You don't need to do anything with the rod to get the quest rewards from the Temple of Helm. You can just rock in, kill the beholder and roll back, so it sounds like you have a bit of a bug in your game I'm afraid. Try reloading a couple of times, or if possible reload a save from before that.