Why isn't the last if statement running after the end. It seems to be getting stuck at something??

It seems you got confused with the tabbing and forgot an elseif by the tool. I think I also got rid of an extra end. I think this is what you're wanting to do:

Try this:

--Variables--
local Purchase_Req = game.ReplicatedStorage.Replicators.Shop.Purchase_req
local Audio_Controller = game.ReplicatedStorage.Replicators.Misc.Audio_Controller
local Hammer = game.ReplicatedStorage.Tools.Hammer:Clone()

local Purchase = "Purchase_Sound"
local Err_Sound = "Err_Sound"

local deb = false
--<--->--
Purchase_Req.OnServerEvent:Connect(function(player,tool)
    --local variables--
    local Currency = player:WaitForChild("Currency")
    local Bits = Currency.Bits
    local Own_Hammer = player:WaitForChild("ToolStat").Hammer

    if not deb then 
		deb = true
	    print("under deb")
	    if tool == "Hammer" then
		    if Bits.Value >=10 and Own_Hammer.Value == false then
			    Own_Hammer.Value = true
			    Bits.Value = Bits.Value -10
			    Hammer.Parent = player.Backpack
			    Audio_Controller:FireClient(player,Purchase)
		
		    elseif Bits.Value <10 or Own_Hammer.Value == true then
		    	print("Wrong elseif stateent")
		        Audio_Controller:FireClient(player,Err_Sound)
		    end
		    print("run") --This one--
	    elseif tool == "Shovel" then
print("Shovel")
	    end
    end
    wait(1)
    deb = false
end)

Definitely make use of the tabbing, it will help you line up your if statements. Most people on here won't help you if the code isn't properly formatted (tabbing in code blocks). I actually had to open up a blank studio and tab it myself before I could see the problem. I'm not harping on you or anything, it's just something you need to know if you want to increase the chances of receiving help.