My checkpoint system sets the level of the player to 0 for no apparent reason?

local DataStoreService = game:GetService("DataStoreService")
local myDataStore = DataStoreService:GetDataStore("myDataStore")

game.Players.PlayerAdded:Connect(function(player)
	local char = player.Character or player.CharacterAdded:wait()
	local ack = Instance.new("IntValue")
	ack.Name = "leaderstats"
	local ack2 = Instance.new("IntValue")
	ack2.Name = "Stage"
	ack2.Value = 1
	ack2.Parent = ack
	ack.Parent = player
	local ack3 = Instance.new("IntValue", ack)
	ack3.Name = "Prestige"
	ack3.Value = 0
	local Folder = Instance.new("Folder", player)
	local ack4 = Instance.new("IntValue", player)
	ack4.Name = "Skips"
	ack4.Value = 0
	player:LoadCharacter()
	local ls = player.leaderstats
	local sl = game.Workspace:FindFirstChild(ls.Stage.Value)
	print(sl.Position)
	char.UpperTorso.CFrame = sl.CFrame + Vector3.new(0,3,0)
	local char = player.Character or player.CharacterAdded:wait()
	print(sl.CFrame)
	local data
	local data2
	local success, errormessage = pcall(function()
		data = myDataStore:GetAsync(player.UserId .. "-Stage")
		data2 = myDataStore:GetAsync(player.UserId .. "-Prestige")
		
	end)
	
	if success then
		ack2.Value = data
		local sl = game.Workspace:FindFirstChild(ls.Stage.Value)
		local char = player.Character or player.CharacterAdded:wait()
		if char:WaitForChild("UpperTorso") then
			char:WaitForChild("UpperTorso").CFrame = sl.CFrame + Vector3.new(0,3,0)
			end
		print(sl)
		ack3.Value = data2
	else
		ack2.Value = 1
		warn(errormessage)
	end
	workspace.ChildAdded:Connect(function(obj)
		if obj.Name == player.Name then
			if obj:WaitForChild("UpperTorso") or  obj:WaitForChild("Torso") then
				local sl = game.Workspace:FindFirstChild(ls.Stage.Value)
				obj:WaitForChild("UpperTorso").CFrame = obj:WaitForChild("UpperTorso").CFrame + Vector3.new(0,3,0)
				print(sl.CFrame)
			
			end
			wait()
			if obj:WaitForChild("UpperTorso") or  obj:WaitForChild("Torso") then
				local sl = game.Workspace:FindFirstChild(ls.Stage.Value)
				obj:WaitForChild("UpperTorso").CFrame = sl.CFrame + Vector3.new(0,3,0)
			end
		end
	end)
end)
game.Players.PlayerRemoving:Connect(function(player)
	
	local success, errormessage = pcall(function()
		myDataStore:SetAsync(player.UserId .. "-Stage", player.leaderstats.Stage.Value)
		myDataStore:SetAsync(player.UserId .. "-Prestige", player.leaderstats.Prestige.Value)
	end)
	
	if success then 
		print("Data Saved!")
	else
		warn(errormessage)
	end
end)

If a player has data they will spawn in the right place after dying once. If a player does not have data they will be on stage 0 and fall to their death infinitely.

On line 40: Attempt to index nil with 'CFrame'

local char = player.Character

That's what line 5 should be.

char:WaitForChild("HumanoidRootPart").CFrame = sl.CFrame + Vector3.new(0,3,0)

That's what line 40 should be.

local DataStoreService = game:GetService("DataStoreService")
local myDataStore = DataStoreService:GetDataStore("myDataStore")

game.Players.PlayerAdded:Connect(function(player)
    local char = player.Character or player.CharacterAdded:wait()
    local ack = Instance.new("IntValue")
    ack.Name = "leaderstats"
    local ack2 = Instance.new("IntValue")
    ack2.Name = "Stage"
    ack2.Value = 1
    ack2.Parent = ack
    ack.Parent = player
    local ls = player.leaderstats
	ls:WaitForChild("Stage").Value = 1
    local ack3 = Instance.new("IntValue", ack)
    ack3.Name = "Prestige"
    ack3.Value = 0
    local Folder = Instance.new("Folder", player)
    local ack4 = Instance.new("IntValue", player)
    ack4.Name = "Skips"
    ack4.Value = 0
    local char = player.Character or player.CharacterAdded:wait()
    local sl = game.Workspace:WaitForChild(ls.Stage.Value)
	print(ls.Stage.Value)
    local data
    local data2
	print(ls.Stage.Value)
    local success, errormessage = pcall(function()
        data = myDataStore:GetAsync(player.UserId .. "-Stage")
        data2 = myDataStore:GetAsync(player.UserId .. "-Prestige")
	print(ls.Stage.Value)
    end)

    if success then
		if data ~= nil then
			print(data)
			ack2.Value = data
			if char:WaitForChild("HumanoidRootPart") then
				print("1")
				local sl = game.Workspace:WaitForChild(ls.Stage.Value)
		        char:WaitForChild("HumanoidRootPart").CFrame = sl.CFrame + Vector3.new(0,3,0)
				print(sl)
        
   			end
		else
			local sl = game.Workspace:WaitForChild(ls.Stage.Value)
		end
        local char = player.Character or player.CharacterAdded:wait()
        if char:WaitForChild("HumanoidRootPart") then
			local sl = game.Workspace:WaitForChild(ls.Stage.Value)
			char:WaitForChild("HumanoidRootPart").CFrame = char:WaitForChild("HumanoidRootPart").CFrame + Vector3.new(0,3,0)
            char:WaitForChild("HumanoidRootPart").CFrame = sl.CFrame + Vector3.new(0,3,0)
			print(sl)
			print(sl.Position)
            end
        ack3.Value = data2
    else
		local sl = game.Workspace:FindFirstChild(ls.Stage.Value)
        local char = player.Character or player.CharacterAdded:wait()
        if char:WaitForChild("HumanoidRootPart") then
            char:WaitForChild("HumanoidRootPart").CFrame = sl.CFrame + Vector3.new(0,3,0)
        warn(errormessage)
    end
end
    workspace.ChildAdded:Connect(function(obj)
        if obj.Name == player.Name then
            if obj:WaitForChild("HumanoidRootPart") then
                local sl = game.Workspace:FindFirstChild(ls.Stage.Value)
                obj:WaitForChild("HumanoidRootPart").CFrame = obj:WaitForChild("HumanoidRootPart").CFrame + Vector3.new(0,3,0)
                print(sl.CFrame)

            end
            wait()
            if obj:WaitForChild("HumanoidRootPart") then
                local sl = game.Workspace:FindFirstChild(ls.Stage.Value)
                obj:WaitForChild("HumanoidRootPart").CFrame = sl.CFrame + Vector3.new(0,3,0)
            end
        end
    end)
end)
game.Players.PlayerRemoving:Connect(function(player)

    local success, errormessage = pcall(function()
        myDataStore:SetAsync(player.UserId .. "-Stage", player.leaderstats.Stage.Value)
        myDataStore:SetAsync(player.UserId .. "-Prestige", player.leaderstats.Prestige.Value)
    end)

    if success then 
        print("Data Saved!")
    else
        warn(errormessage)
    end
end)

This is the fixed code.