How to extend function wait() if called twice or more?

Not quite sure what you're asking, but I've come up with a script.

-- Local Script (inside a tool!)
local Tool = script.Parent
local Player = game.Players.LocalPlayer

local RE = game:GetService("ReplicatedStorage"):WaitForChild("RemoteEvent",10)
Tool.Activated:Connect(function()
    RE:FireServer()
end)

--[[
#################################################################################
]]

-- Script
local Players = {}

game.ReplicatedStorage.RemoteEvent.OnServerEvent:Connect(function(player)
    local PlrTab = Players[player]
    if(PlrTab ~= nil) then
        local deClick = PlrTab.Clicked
        if(deClick == false) then
            PlrTab.Clicked = true
            print("Clicked!!!, Starting process")
            player.Time.Value = true
            wait(5)
            player.Time.Value = false
            print("Stopping Ignoring Clicks for now!")
            PlrTab.Clicked = false
        else
            print("All ready Clicked ignoring...")
        end
    end
end)

game.Players.PlayerAdded:Connect(function(plr)
    --[[ debugging ]]
    local Time = Instance.new("BoolValue",plr)
    Time.Name = "Time"
    Time.Value = false
    --[[ debugging ]] 

    -- Global table hookup
    Players[plr] = {
        Clicked = false
    }
end)
game.Players.PlayerRemoving:Connect(function(plr)
    -- remove the player thats leaving from global table
    if(table.find(Players,plr) ~= nil) then
        Players[plr] = nil
    end
end)

This script logs every player that joins the game and adds your Time bool value to each player. The server side script then waits for a player to activate or click with the tool to change the Time.Value from false to true, as you had, then waits 5 seconds before changing it back to false.

I've made it ignore any other clicks made by a player. Thus stopping the click spam. I've also allow other players to change their Time bool values without locking up the system until the Clicked Value gets changed back to false.

Let me know if you need anything :)