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Based on the fact that Special Ops Mission exists in conjunction with Brainstorm, does that mean you cannot play a Secret Action using a battle card effect (like those on Multi-Mission Gear or Brainstorm) unless it specifically says so?

Things that effect actions also effect secret actions, which are a subset of actions.
Source: Wizards of the Coast (2019-04-26)    【Link to Ruling】
Tags: Secret Action