I have a secret command on MCGalaxy, but I want to hide it from people so they can't do /help on it or accidentally find the command. Also, as a bonus, is there a way to prevent them from using / again to see the command?

make a handler for OnPlayerCommandEvent like this, set p.cancelcommand = true; (so it dosent show Unknown command "secret") and p.lastCMD = ""; (to prevent the player from using / to run it again)

but why do you even want to make a command that dosent appear on /help and hides itself?

Because it gives a secret award and if someone finds it in /help and runs it, then they wouldn't have 'earned' that award.