How to make it where you can accidentally burn food when cooking?

You can use coroutines to make a wait and not pause the thread (or just put the wait at the end)

Also, using MouseClick will always do a new function and putting a wait wont work.

Use this code:

local connection
function onClicked()

local ToolNames = {"CookedBacon", "Item", "Item"}-----put name of the tool has to be exact exact name (remove the words items but not (") keep (")Between (" ") put item name for EX: "Glock 17"
local Storage = game:GetService("ServerStorage")----Put the tool item in serverstorage (cars,hats,and clothing will not work only tools work like guns and such)


local Part = script.Parent
local ClickDetector = Part:WaitForChild("ClickDetector")
local alreadyFinished = false --// a way to know if the player has already clicked
coroutine.resume(corutine.create(function()

                wait(3)
if alreadyFinished == false then
                script.Parent.SurfaceGui.TextLabel.Text = "BURNT"
                script.Parent.Parent.BurntBacon.Transparency = 0
                script.Parent.Parent.BurntBacon.Smoke.Enabled = true
                script.Parent.Parent.Baconn.Transparency = 1
end
end))
ClickDetector.MouseClick:connect(function(Player)
    if Player and Player.Character then
        local Backpack = Player:WaitForChild("Backpack")
        for i = 1, #ToolNames do
            local Tool = Storage:FindFirstChild(ToolNames[i])
            if Tool then
                Tool:clone().Parent = Backpack
                script.Parent.Transparency = 1
                script.Parent.SurfaceGui.Enabled = false
                script.Parent.Parent.Transparency = 1
                script.Parent.Parent.Baconn.Transparency = 1
alreadyFinished = true

            end
        end
    end
end)



end 
  connection = script.Parent.ClickDetector.MouseClick:Connect(onClicked) -- connect is deprecated use Connect instead