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I am playing Nightbird in alt mode. My opponent plays Brainstorm and 2 follow-up actions. I reveal a Secret Action to stop 1 of the follow-ups. Does my opponent still take 3 damage?

Yes. Even when cancelled by an action such as Infiltrate, Jam Signals, or Overrule, a card is still played and an effects that refer to cards, or number of cards, being played still occur. Another example would be Thundercracker, Mach Warrior's bot mode effect.
Source: Aequitas (2022-08-23)    【Link to Ruling】
Tags: Nightbird, Enigmatic Agent