Perhaps because of its failure, the Brain-wave Scanner wasn't used for the following months, and after Venom's death, Cobra nearly forgot about the machine. When Cobra Commander was almost assassinated by his own son, Billy, the Brain-wave Scanner was used as a way to interrogate the boy. Use of the Scanner was actually suggested by Zartan, who had heard rumors of the machine in the criminal underground for years. Like Snake-Eyes, Billy was strong-willed enough to block the machine from discovering the identities of his co-conspirators, instead drudging up the painful memories of his father's rise to power. Before too much could be revealed about his past the Commander unstrapped Billy from the machine. The device was not used again on Billy, since he was freed by Storm Shadow. A short time later, Cobra Commander allowed the Cobra scientist Dr. Mindbender access to the Brain-wave Scanner during his creation of Serpentor. The machine was used to scan information about Cobra from Mindbender's brain and to place it in the newly-formed mind of Serpentor (Destro and the Baroness neglected to tell Mindbender how painful the scanning process was). When the Joe team member Ripcord was captured by Cobra, he was strapped into the machine and used to give Serpentor knowledge of the team's tactics. After the creation of Serpentor, Mindbender made his own modifications to the Scanner, making it smaller and more efficient. In the nation of Sierra Gordo, the new Scanner was being kept in Cobra's Terror-Drome. A Joe made to look like Flint was captured there and strapped into the machine for interrogation. Mindbender soon discovered that the Joe was actually Snake-Eyes in disguise. Snake-Eyes again fought the machine until he was rescued by the Joes. Unfortunately, Snake-Eyes was captured soon after and brought to the Cobra Consulate building in Manhattan. A lab was set up there for Mindbender and he now intended to get all the information out of Snake-Eyes he could. But after his previous ordeals with the device, Snake-Eyes used a ninja calming technique to disrupt the machine, causing it to destroy itself. Again, Snake-Eyes slipped through the fingers of Cobra' chief scientist, escaping with Scarlett's and Storm Shadow's help.

Years later, the Scanner resurfaced. Zarana used it to brainwash Joes Clutch and Rock & Roll when they were held prisoner in Broca Beach. This time, it was used to plant information in their minds instead of extract it. After their rescue, the post-hypnotic suggestions planted by Zarana nearly sent Clutch and Rock & Roll into a berserker rage inside Joe headquarters before their own sense of morality overrode the programming. When Cobra Commander returned from a long absense from Cobra, he used the Scanner to subjugate the American town of Millville, now using a smaller helmet-sized scanner. Some time later, the Joes freed the townspeople from Cobra's control. Over the next few years, the Commander used the Scanner in various forms to brainwash the Baroness into attempting to kill Destro, and later to take control of Storm Shadow, the Baroness and Billy in Trans-Carpathia. The Joes failed to rescue these victims of the Scanner, though it now appears that they eventually broke free.

The Brain-wave Scanner remains a symbol of Cobra's casual disregard for anyone that could get in the way of their plans, and has made certain that Dr. Venom's evil legacy continued for many years. (GI 10, 38, 49, 50, 54-56, 90-100, 145-151; YB 3)