I vividly remember a cartoon from the 90s or early 00s where the female character appears to double-cross the good guys, only to actually help them at the last minute. Then the bad guy is like "I thought you were a double agent!" and she says "Wrong, I'm a triple agent!" (or something like that). Then the villain just looks confused and has to count on his fingers before getting angry.

I thought for sure it was the blue lady from the movie "Buzz Lightyear of Star Command: The Adventure Begins". (Could have been the show, but I didn't watch much of the show.) I even checked the subtitle file for the movie when I couldn't find the scene, and the only use of the word "agent" in that movie is when Warp Darkmatter says "Hey! I'm Zurg's number-one agent!"

I've started to think it might be from a Kim Possible episode. But I have no leads on which one it might be, if it's even from that show. Googling "Kim Possible" and "triple agent" both in quotes didn't help.