How would I add a hotkey to this fly script?

Since Mouse.KeyDown is deprecated, you must use UserInputService. Also, I remade your code to look nicer and more readable.

local UserInputService = game:GetService("UserInputService")

local Player = game.Players.LocalPlayer
local Character = Player.Character or Player.CharacterAdded:Wait()
local HumanoidRootPart = Character:WaitForChild("HumanoidRootPart")

local e1
local e2
local Fly = false
local Speed = 0
local keys = {a = false,d=false,w=false,s=false}

local function start()
    if not Fly then
        Fly = true
    else
        Fly = false
    end

    local pos = Instance.new("BodyPosition")
    local gyro = Instance.new("BodyGyro")

    pos.Name = "EPIXPOS"
    pos.maxForce = Vector3.new(math.huge, math.huge, math.huge)
    pos.position = HumanoidRootPart.Position
    gyro.maxTorque = Vector3.new(9e9, 9e9, 9e9)
    gyro.cframe = HumanoidRootPart.CFrame

    pos.Parent = HumanoidRootPart
    gyro.Parent = HumanoidRootPart
    repeat
        wait()
        Character.Humanoid.PlatformStand = true
        local new = gyro.cframe - gyro.cframe.p + pos.position
    if not keys.w and not keys.s and not keys.a and not keys.d then
        Speed = 1
    end

    if keys.w then
        new = new + workspace.CurrentCamera.CoordinateFrame.lookVector * Speed
        Speed=Speed+0.01
    end

    if keys.s then
        new = new - workspace.CurrentCamera.CoordinateFrame.lookVector * Speed
        Speed = Speed+0.01
    end

    if keys.d then
        new = new * CFrame.new(Speed,0,0)
        Speed=Speed+0.01
    end

    if keys.a then
        new = new * CFrame.new(-Speed,0,0)
        Speed = Speed+0.01
    end

    if Speed > 5 then
        Speed = 5
    end

    pos.position=new.p

    if keys.w then
        gyro.cframe = workspace.CurrentCamera.CoordinateFrame*CFrame.Angles(-math.rad(Speed*15),0,0)
    elseif keys.s then
        gyro.cframe = workspace.CurrentCamera.CoordinateFrame*CFrame.Angles(math.rad(Speed*15),0,0)
    else
        gyro.cframe = workspace.CurrentCamera.CoordinateFrame
    end

    until not Fly

    if gyro then gyro:Destroy() end
    if pos then pos:Destroy() end
    flying = false
    Character.Humanoid.PlatformStand=false
    Speed = 0
end

UserInputService.InputBegan:Connect(function(Input, GameProcess)
    if GameProcess then return end
    if not HumanoidRootPart or not HumanoidRootPart.Parent then flying = false e1:disconnect() e2:disconnect() return end
    if Input.KeyCode == Enum.KeyCode.W then
        keys.w = true
    elseif Input.KeyCode == Enum.KeyCode.S then
        keys.s = true
    elseif Input.KeyCode == Enum.KeyCode.A then
        keys.a = true
    elseif Input.KeyCode == Enum.KeyCode.D then
        keys.d = true
    end
end)

UserInputService.InputEnded:Connect(function(Input, GameProcess)
    if GameProcess then return end
    if not HumanoidRootPart or not HumanoidRootPart.Parent then flying = false e1:disconnect() e2:disconnect() return end
    if Input.KeyCode == Enum.KeyCode.W then
        keys.w = false
    elseif Input.KeyCode == Enum.KeyCode.S then
        keys.s = false
    elseif Input.KeyCode == Enum.KeyCode.A then
        keys.a = false
    elseif Input.KeyCode == Enum.KeyCode.D then
        keys.d = false
    end
end)

UserInputService.InputBegan:Connect(function(Input, GameProcess)
    if GameProcess then return end
    if Input.KeyCode == Enum.KeyCode.F then -- Change "F" to the letter for activating the fly
        start()
    end
end)

If it helped, accept the answer! :D

UserInputService Mouse.KeyDown is deprecated. Also, I noticed this was all one script so, here is a link to the roblox dev documentation.

https://developer.roblox.com/en-us/api-reference/class/UserInputService

Roblox's Server to Client model https://developer.roblox.com/en-us/articles/Roblox-Client-Server-Model https://developer.roblox.com/en-us/articles/Remote-Functions-and-Events