The number prints as two but the player isn't given the sword?

It has to do with where you put the word "end".

Let me fix your indentation:

game.ReplicatedStorage.CloneTool.OnServerEvent:Connect(function(player)
	local number = math.random(1,2)
	print(number)
	if number == 1 then
		local Tool = game.ServerStorage.ClassicSword
		local Part = script.Parent
		local Clone = Tool:Clone()
		Clone.Parent = player.Character
		if number == 2 then
			local Tool = game.ServerStorage.Sword
			local Part = script.Parent
			local Clone = Tool:Clone()
			Clone.Parent = player.Character
		end
	end
end)

Looking at your code, the conditional statement that checks to see if the number is 2 is inside of the conditional statement which checks to see if the number is 1, meaning that the line where it checks to see if the number is 2 will not be reached if the number is 2, because the conditional statement before it would not evaluate to true.

This is how it should be:

game.ReplicatedStorage.CloneTool.OnServerEvent:Connect(function(player)
	local number = math.random(1,2)
	print(number)
	if number == 1 then
		local Tool = game.ServerStorage.ClassicSword
		local Part = script.Parent
		local Clone = Tool:Clone()
		Clone.Parent = player.Character
	elseif number == 2 then
		local Tool = game.ServerStorage.Sword
		local Part = script.Parent
		local Clone = Tool:Clone()
		Clone.Parent = player.Character
	end
end)