My spaghetti code

using UnityEngine;
using UnityEngine.UI;
using System.Collections;
using UnityEngine.EventSystems;

public class GameController : MonoBehaviour {
    public Player playerPrefab;
    Player player;
    public Image blackFade;
    float fadeSmoothing;
    public Slider playerHealthSlider;
    public Slider playerAmmoSlider;
    public Camera mainCamera;

    public GameObject pauseButtons;
    public GameObject menuButtons;
    public GameObject optionButtons;
    public GameObject stageSelectButtons;

    StagesInfo[] stageInfo;
    GameObject currentStage;

    public Canvas canvas;
    public GameObject[] dropItems;
    public GameObject[] stages;
    public static GameController instance;
    Vector2 directionalInput;
    public static bool menuOn = true;
    public static bool gameIsPaused = false;
//  bool gameIsOn;



    void Awake ()
    {
        instance = this;
        mainCamera = Camera.main;
        stageInfo = new StagesInfo[stages.Length];
    }

    // Use this for initialization
    void Start () {
        EventSystem.current.SetSelectedGameObject(GameObject.Find("Menu Buttons/Start Game Button"));
    }

    // Update is called once per frame
    void Update () {
        if (!menuOn)
        {
            HandleSlideBars();
        }
        print(stageInfo[1].heartStatus);
    }

    void HandleSlideBars()
    {
        playerHealthSlider.value = player.currentHealth;
        if(player.currentWeapon != 0)
        {
            playerAmmoSlider.gameObject.SetActive(true);
            playerAmmoSlider.value = player.bulletAmmo[player.currentWeapon];

        } else
        {
            playerAmmoSlider.gameObject.SetActive(false);
        }
    }

    void InitializeGUI()
    {
        playerHealthSlider.maxValue = player.startingHealth;
        playerAmmoSlider.maxValue = 100;
        playerAmmoSlider.gameObject.SetActive(false);
    }

    public void OnStartGameButtonPress()
    {
        StartCoroutine(Fade(true, 1));
        foreach(StagesInfo element in stageInfo)
        {
            print("We in here nigga");
            element.Initialize();
        }
        StartCoroutine(StageSetup(0,2));

    }

    public void OnOptionsButtonPress()
    {
        if (!optionButtons.activeSelf)
        {
            menuButtons.SetActive(false);
            optionButtons.SetActive(true);
            EventSystem.current.SetSelectedGameObject(GameObject.Find("Option Buttons/Back Button"));
        } else
        {
            optionButtons.SetActive(false);
            menuButtons.SetActive(true);
            EventSystem.current.SetSelectedGameObject(GameObject.Find("Menu Buttons/Options Button"));
        }
    }

    public void OnGamePauseBackButtonPress()
    {
        gameIsPaused = (gameIsPaused) ? false : true;
        GameController.menuOn = gameIsPaused;
        Time.timeScale = (gameIsPaused) ? 0 : 1;
        instance.pauseButtons.SetActive(false);
    }

    public static void OnGamePause()
    {
        gameIsPaused = (gameIsPaused) ? false : true;
        GameController.menuOn = gameIsPaused;
        Time.timeScale = (gameIsPaused) ? 0 : 1;
        if (gameIsPaused)
        {
            instance.pauseButtons.SetActive(true);
            EventSystem.current.SetSelectedGameObject(GameObject.Find("Pause Buttons/Back Button"));
        } else
        {
            instance.pauseButtons.SetActive(false);
        }
    }

    public void OnExitButtonPress()
    {
        Application.Quit();
    }

    public void StageEndWrapper()
    {
        instance.StartCoroutine(instance.OnStageEnd(false));
    }

    public static void StageEndWrapper(bool completed)
    {
        instance.StartCoroutine(instance.OnStageEnd(completed));
    }

    public IEnumerator OnStageEnd(bool completed)
    {
        StageInfo endingStageInfo = currentStage.GetComponent<StageInfo>();
        menuOn = true;
        if (endingStageInfo.stageID != 0)
        {
            print("Stage ending, updating stageInfo");
            stageInfo[endingStageInfo.stageID].Update(endingStageInfo.heartStatus, endingStageInfo.armorStatus, (stageInfo[endingStageInfo.stageID].completionStatus == true)?true:completed);
        }
        yield return new WaitForSeconds(5);
        StartCoroutine(Fade(true, 1));
        yield return new WaitForSeconds(4);
        if (player != null)
        {
            Destroy(player.gameObject);
        }
        Destroy(currentStage);
        playerHealthSlider.gameObject.SetActive(false);
        OnStageSelectButtonPress();
    }


    public void StageSetupWrapper(int stageID)
    {
        StartCoroutine(Fade(true, 1));
        StartCoroutine(StageSetup(stageID, 0));
    }

    public void OnStageSelectButtonPress()
    {
        StartCoroutine(Fade(false, 1));
        menuButtons.SetActive(false);
        stageSelectButtons.SetActive(true);
        EventSystem.current.SetSelectedGameObject(GameObject.Find("Stage Selection Buttons/Stage 1 Button"));
    }

    public IEnumerator StageSetup(int stageID, int checkpoint)
    {
        yield return new WaitForSeconds(3);

        menuButtons.SetActive(false);
        menuOn = false;
        Instantiate(stages[stageID], new Vector3(0,0,-0.69f), Quaternion.identity);
        Instantiate(playerPrefab, stages[stageID].GetComponent<StageInfo>().checkpoints[checkpoint], Quaternion.identity);
        player = GameObject.FindWithTag("Player").GetComponent<Player>();
        currentStage = GameObject.FindWithTag("Stage");
        StageInfo currentStageInfo = currentStage.GetComponent<StageInfo>();
        if (currentStageInfo.stageID != 0)
        {
            print(stageInfo[currentStageInfo.stageID].heartStatus);
            currentStageInfo.Initialize(stageInfo[currentStageInfo.stageID].heartStatus, stageInfo[currentStageInfo.stageID].armorStatus, stageInfo[currentStageInfo.stageID].completionStatus);
        }
        playerHealthSlider.gameObject.SetActive(true);
        InitializeGUI();
        mainCamera.GetComponent<CameraFollow>().GetTarget(player.GetComponent<Controller2D>());

        StartCoroutine(Fade(false, 1));
    }

    IEnumerator Fade(bool fadeIn, float fadeSpeed)
    {
        float currentAlpha = blackFade.color.a;
        while(blackFade.color.a <= 1 && blackFade.color.a >= 0)
        {
            if (fadeIn)
            {
                currentAlpha += fadeSpeed * Time.deltaTime;
            } else
            {
                currentAlpha -= fadeSpeed * Time.deltaTime;
            }
            blackFade.color = new Color (0,0,0,currentAlpha);

            yield return new WaitForFixedUpdate();
        }
        blackFade.color = new Color (0,0,0,(blackFade.color.a > 1)?1:0);
    }

    struct StagesInfo
    {
        public bool heartStatus;
        public bool armorStatus;
        public bool subItemStatus;
        public bool completionStatus;

        public void Initialize()
        {
            print("It initialized");
            heartStatus = true;
            print(heartStatus);
            armorStatus = true;
            completionStatus = false;
            print(heartStatus);
        }

        public void Update(bool heartUpdate, bool armorUpdate, bool completionUpdate)
        {
            heartStatus = heartUpdate;
            armorStatus = armorUpdate;
            completionStatus = completionUpdate;
        }
    }

    public static GameObject GetDropItem()
    {
        int randomNumber = Random.Range(0,9);
        switch (randomNumber)
        {
        case 0:
            return instance.dropItems[0];
        case 1:
            return instance.dropItems[1];
        case 2:
            return instance.dropItems[2];
        case 3:
            return instance.dropItems[3];
        default:
            return null;
        }
    }
}