Part two of four: Captain O'Shea returns to a home he once knew, only to find secrets revealed from a people known solely from myths and legends. A search on New Harvest, a Federation world, soon becomes an intelligence gathering mission as startling parallels are drawn, and the Starhaven crew must journey close to enemy territory to protect the Federation's future.

Developed similarly as the preceding issue, more than 95% of the comic panels are not merely direct screen-captures from The Animated Series television show, but are entirely new graphics or intricate composites of existing characters, ships, and backgrounds to create never-before-seen images. Eyes of New Harvest brings readers even more unique scenes from the animated Star Trek Universe.