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Secret Missions are things in Club Penguin that don't come out as often as they should. THey first came out once every 2 months, but it has been over 6 months since the last one (Waddle Squad)

In order to d a secret mission you need to be a secret agent. They take about 5-30 minutes to complete and usually take skill and logic to complete (This has been becoming more absent ever since Disney purchased it). There are no awards you get from doing secret missions that you can show other people in the game (Like clothes or Pins) but you do get badges and stuff (which you cannot show people for some strange reason)