The Avengers: Earth's Mightiest Heroes animated series has been loosely based on the Marvel comics. We wouldn't expect a brand new series to follow close to fifty years of comic book continuity to the letter. Throughout the current first season, there have been some surprising twists.
If you saw the brand-new episode of The Avengers: Earth's Mightiest Heroes this Sunday up to the end, you watched the major spoiler in the end... oh that's right: all of this article is under SPOILER ALERT!!!!
Now that you're aware of the spoilers here, I can proceed by saying that the HYDRA's leader, Baron Von Strucker, righthand woman, Viper is a SKRULL. She was discovered by Nick Fury and Bobbi Morse (Mockingbird), at the end of the episode, in a style very similar to the way the New Avengers found out Elektra was a Skrull back in New Avengers vol.1 #36-37.
If you've been following the animated series, you know the writers have inspired themselves in recent storylines, as seen in the first couple episodes, adapting the New Avengers origin into the Avengers' in the cartoon, with the mass supervillain breakout.
Now the inspiration comes from the Secret Invasion story arc by Brian Michael Bendis. The extent of this event on the small screen is yet to be seen but I hope it will be as fun to follow as the amazing comics by Marvel.