Elektra Revealed to be a Skrull – New Avengers # 31
Liked Captain Marvel (liked not loved) and the Skrulls managed to be a cool gang in the movie, so why not do a series of posts on them. Let’s do Secret Invasion which begins showing its deep secrets in the pages of New Avengers # 31 by Brian Michael Bendis and Leinil Yu.
So the gist of this whole arc is that Maya Lopez aka Echo had been taken by The Hand in Japan. And she needed bailing out because she was Captain America’s operative in Japan before the events of Civil War. With Captain America “dead” and Iron Man having his own team who does not care about Echo, a new New Avengers team is formed by Luke Cage which consists of Iron Fist, Doctor Strange, Wolverine, Spider-Man, Spider-Woman and Ronin. In Japan, they do battle with The Hand and Silver Samurai a number of times before ultimately winning against Elektra.
What happens is Doctor Strange manages to free Maya from The Hand’s conditioning, so she’s a good guy again. Iron Fist distracts her enough for Strange to use his magic and remove the spell they put on Echo. Really pissed off at Elektra for both losing and for being turned into a pawn, Echo rushes Elektra and lands a killing blow on her (see above).
With their mistress gone, the rest of the Hand ninjas disperse, leaving the body of Elektra with the New Avengers.
That they didn’t encounter Elektra at all. They just fought and killed a Skrull pretending to be Elektra AND ruling Japan’s Hand syndicate.
To answer Danny Rand’s question, this starts the months worth of storytelling in various Avengers books to detail what the Skrulls have been up to and who they have abducted and replaced. This also culminates in the now-classic story Secret Invasion.