Cloned GUI wont go away?

Ok, what you've done is a silly but common mistake. You have defined phoneactive at the start of the script, but that value will never change once it's been defined even if later the GUI does exist. What you need to do is move then inside the key pressed event to make it check whether the phone is active when it's pressed. Your code should look like this:

local guis = game.ReplicatedStorage.GUIs
local player = script.Parent.Parent

function onKeyPress(inputObject, gameProccessedEvent)
    if not gameProccessedEvent then -- If not using an event, run this code
        if inputObject.KeyCode == Enum.KeyCode.G then
            local phoneactive = script.Parent:FindFirstChild("Phone")
            if phoneactive then
                script.Parent.Phone:Destroy()
            else
                local help = guis.Phone:Clone()
                help.Parent = player.PlayerGui
                player.PlayerGui.PlayerAudio.Pullup:Play()
            end
        end
    end
end

game:GetService("UserInputService").InputBegan:connect(onKeyPress)

Alright brother. Here ya go. When you use this script, what you have to do is have a ScreenGui, within the screengui, have the frame you want to be opened and name that Frame and this script goes into a Local Script. The Local Script's parent needs to be the screengui. Then bam. It works.

local GUI = script.Parent
local Frame = GUI:WaitForChild("Frame")
local Buttons = Frame:GetChildren()
local Player = game.Players.LocalPlayer
local Mouse = Player:GetMouse()




Mouse.KeyDown:connect(function(key)
    if key == "l" then
        Frame.Visible = not Frame.Visible
    end
end)

If you have any questions just come ask me.