How do I make it so that a player gets points when they click a part with a tool out?

Alright, so this is personally how I would do this (put a remote event in ReplicatedStorage named RemoteEvent btw) here's the script (explanations are inside the script)

-- local script
-- put this script inside your tool
-- this is important - if you have more than one part to make one dirt stain, group all of your parts and name the group DirtStain (doesn't matter what the children of the group are called)
-- also it doesn't matter if you only have one part to make one dirtstain, just group it by itself and name it DirtStain for it to work

local RPS = game:GetService("ReplicatedStorage") -- getting ReplicatedStorage
local RemoteEvent = RPS:WaitForChild("RemoteEvent") -- defining the remote event (change the name of it if needed)
local Player = game.Players.LocalPlayer
local Mouse = Player:GetMouse()
local Equipped = false
local Tool = script.Parent
local DirtStains = game.Workspace.DirtStains -- folder that holds dirt stains

Mouse.Button1Down:Connect(function()
    if Equipped then -- if tool is equipped
        if Mouse.Target.Parent.Name == "DirtStain" then -- if group of target is named dirtstain then
            RemoteEvent:FireServer(Mouse.Target.Parent) -- firing a server event that sends the information of the dirt stain
        end
    end
end)

Tool.Equipped:Connect(function() -- function to check if tool is equipped
    Equipped = true
    print("Equipped")
end)

Tool.Unequipped:Connect(function() -- function to check if tool is not equipped
    Equipped = false
    print("Unequipped")
end)

and here is the server script, put this inside ServerScriptStorage:

-- put this script inside ServerScriptStorage

local RPS = game:GetService("ReplicatedStorage") -- getting ReplicatedStorage
local RemoteEvent = RPS:WaitForChild("RemoteEvent")
local Time = 5 -- how long it will take for the DirtStain to respawn

RemoteEvent.OnServerEvent:Connect(function(Player, DirtStain)
    for i,v in pairs(DirtStain:GetChildren()) do -- getting children of the group
        v.Transparency = 1 -- makes all children of the group completely transparent
    end
    local Points = Player.leaderstats:WaitForChild("Points")
    if DirtStain.Name == "DirtStain" then
        DirtStain.Name = "Clean" -- changing "DirtStain" to "Clean" so you can't spam collect points
        Points.Value = Points.Value + 1 -- gives you a point
        wait(Time)

        -- IF YOU WANT THE DIRTSTAIN TO RESPAWN KEEP THIS, OTHERWISE DELETE THIS VVV
        for i,v in pairs(DirtStain:GetChildren()) do -- getting children of the group
            v.Transparency = 0 -- makes all children of the group opaque
        end
        DirtStain.Name = "DirtStain"
        -- IF YOU WANT THE DIRTSTAIN TO RESPAWN KEEP THIS, OTHERWISE DELETE THIS ^^^
    end
end)

Here is the final product: https://streamable.com/mpca4t

I didn't make leaderstats so I used print to show how many points I would have

If you have any questions please ask me ASAP so I can answer them, if you found this helpful please accept my answer.

First Of All, We need to know if the player actually cleans up the mess, So after you clean it up an event will fire and if that event is fired then in a server script the value of the points increases, and then define the variable of dirt in the script and set the transparency to 1. Please upvote this if it works. Here are the scripts for if you're confused.

--Code here
Animation:Play()
local event = Instance.new("RemoteEvent", game.ReplicatedStorage)
event.Name = "CleanedUp"
event:FireServer(game.Players.LocalPlayer)
--Code here

game.ReplicatedStorage:WaitForChild("CleanedUp").OnServerEvent:Connect(function(Player)
       local points = Player.leaderstats:WaitForChild("Points")
       points.Value = points.Value + 1
       local Dirt = DirtVariable
       Dirt.Transparency = 1
end