The action in Gray Lensman picks up immediately where Galactic Patrol left off, in the middle of the battle to destroy Helmuth's Main Base and, it is hoped, fully end the threat of Boskone. After the base falls, Kinnison finds some clues that lead him to think that Helmuth was perhaps not the head of Boskone after all.

The clues lead Kinnison to mount an expedition aboard the newly constructed super-dreadnought Dauntless, into the Second Galaxy where he thinks the true head of Boskone might reside.

The Dauntless locates a planet under attack and comes to its aid, destroying the Boskonian forces and discovering that the entire planet is capable of going "free" (that is, inertialess, the method used in the Lensman books to achieve interstellar and intergalactic space travel). The Lensman returns to the First Galaxy with the space-faring planet and its grateful residents.