It's April, 1993 and Cobra Commander's personal assassin Whisper has traveled to a remote Indonesian island to continue her training.

Dr. Mindbender and a small group of Cobra operatives join her, continuing some research long thought abandoned, unaware that a secret team of G.I. Joe infiltrators has landed and is preparing to strike.

As it all comes crashing down, Whisper may be the only one who can save the day, but when she runs across a mysterious young man, it seems like there are more questions than answers. She suspects he can explain it all, if only she could get him to speak...