Irwin Allen was a producer who, like most in his profession, never let a frame of film go to waste -- his motto was, if something already in the can could be used to help put together key elements of a decent new story, pull it out and use it (even if it meant tailoring all kinds of details of the new story to fit the stock footage)! In this case, there were two stories mashed together in one episode, sort of like what Universal was known for doing in combining episodes of series like Tales of Fargo or The Virginian into feature-length films.
The better of the two stories is one of grief and revenge. Seaman Benson (Paul Carr. who had previously played a crew member named Clark in episodes of the series) is driven to plan the murder of Cmdr. Lee Crane (David Hedison), as he blames the latter for giving the order that killed Benson's best friend, Grady who, as a favor to Benson, had taken over the latter's assigned shift in a section of the ship that ends up flooded). The opportunity for revenge arises as Crane and the Seaview are trying to find and rescue Admiral Nelson (Richard Basehart) and Chief Sharkey (Terry Becker), who have become stranded on an island where large prehistoric creatures are roaming around. As a result, not for the first time, Irwin Allen called up footage from his 1960 feature THE LOST WORLD; and he also utilized tinted black-and-white footage from the Season One Voyage episode "Submarine Sunk Here" (one of the series' high points, incidentally) to depict Grady's death.
The LOST WORLD footage seems hokey today but in the mid-1960s it looked great on TV, and the psychological side of the story -- especially the interactions between Benson and Kowalski (Del Monroe) -- holds the viewer's interest. Additionally, this was the episode in which the writers began exploring the notion of a friendship and bond between Nelson and Sharkey that would become an ongoing feature in subsequence scripts. And to top it off, for once, stuntman/extra Ron Stein actually gets a line of dialogue, though he is still uncredited.
Later entries in the series would turn to similar recycling of material, but at this point the writing and acting were still pretty fresh, and it works.