My gun bullets are going the wrong way, Any way to stop this?

Assuming you will be using something to 'push' the bullet forward. Instead of Bullet.CFrame + Bullet.CFrame, try CFrame.new()

CFrame.new(startPosition, lookVector) -- First parameter being where it should be positioned, second being where it should be pointing. So, applying it to your script should look something like this:

script.Parent.Fire.OnServerEvent:Connect(function()
    local bullet = Instance.new("Part",workspace)
    bullet.BrickColor = BrickColor.Random()
    bullet.Anchored = true
    bullet.Size = Vector3.new(0.5, 0.5, 1)
    bullet.Shape = "Cylinder"
    for i = 1,100 do
        if bullet == nil then
            break
        end
        print (bullet.Position)
	-- Change lookVector to where you want the bullet to face. lookVector also uses position.
        bullet.CFrame = CFrame.new(script.Parent.Handle.Pointer.Position + Vector3.new(0,0,1), lookVector)
        if i == 99 then
            bullet:Destroy()
        end
        wait ()
    end
end)

You can read more up on CFrame here and here.