Part one of four: What begins as an investigation into the disappearances of two Starfleet ships quickly escalates into a confrontation of galactic proportions. More than a weapon, what is at stake is the altering of the balance of power in the entire quadrant and beyond. The crew soon realizes a Federation enemy holds the key to unlocking a technological marvel, and the Starhaven may not be able to escape destruction!

Not counting text or speech bubbles, approximately 900 individual elements composed the comic book panels in Perils of Waves and War. More than 95% of the comic panels are not merely direct screen-captures from The Animated Series TV show, but are entirely new graphics or intricate composites of existing characters, ships, and backgrounds to create never-before-seen images. Though the issue may be read as a standalone "pilot episode" story, it also serves as the introduction to the four-issue story arc of the series.