Why Is This Not Working?

The pc.GetComponent<???> aren’t being disabled.

void Start () {
        playerSpawnPointPos = ChooseSpawnPoint.PickSpawnPoint(Application.loadedLevelName.ToString(), PlayerPrefs.GetString("Last Zone", "Town"));
        playerCharacter = (GameObject)Resources.Load("Prefabs/Player Character Prefab");
        pc = Instantiate(playerCharacter, playerSpawnPointPos, Quaternion.identity) as GameObject;
        if(Application.loadedLevelName.ToString() == "Main Menu" || Application.loadedLevelName.ToString() == "Character Generation"){
            pc.GetComponent<Movement>().enabled = false;
            pc.GetComponent<BallThrow>().enabled = false;
            pc.GetComponent<Encounter>().enabled = false;
        }
        pc.name = "Player Character";
        pcScript = pc.GetComponent<PlayerCharacter>();
        cam = Instantiate(mainCamera, Vector3.zero, Quaternion.identity) as GameObject;
        if(Application.loadedLevelName.ToString() != "Main Menu" || Application.loadedLevelName.ToString() != "Character Generation"){
            LoadCharacterData();
            headsUpDisplay = (GameObject)Resources.Load("Prefabs/HUD Prefab");
            eventSystem = (GameObject)Resources.Load("Prefabs/Event System Prefab");
            Instantiate(headsUpDisplay, Vector3.zero, Quaternion.identity);
            Instantiate(eventSystem, Vector3.zero, Quaternion.identity);
        }
        pcScript.LastZone = Application.loadedLevelName.ToString();
        SaveCharacterData();
    }

I would say your if conditions are not being met.

They’re being met, because I’m running the Main Menu scene while I’m testing this.

I would print out the loaded level value to be sure, because the code looks fine

Done. It prints out as Main Menu. (Of course in the editor the new level is never really loaded so it doesn’t change to Character Generation, but since at the initial Start it WAS Main Menu, those components should be disabled.)

Looks like you need to refactor. I found that code particularly troublesome to follow. When bugs like this come along perhaps rewrite it a different way.

Which part was hard to follow? I’m not assuming that it’s not hard to follow, I’m just wondering where you stopped being able to follow along.