While it seemed that the Secret Society disbanded, Gorilla Grodd actually expanded the organization by recruiting several supervillains in the same fashion as the Justice League, renaming themselves as the Legion of Doom. Unlike the League, however, members were allowed to pursue their own operations, be it robbery or whatever, but they had the option of calling upon the organization for assistance should superheroes interfere. For such service, the standard fee was 25% of the relevant job's gross earnings.
Members of the Legion had run-ins with the League several times, but managed to leave the League in the dark as to the organization's existence. Behind the scenes, Gorilla Grodd led the Legion until Lex Luthor usurped leadership. Given that Grodd had just attempted to turn all humanity into apes, included the Legionnaires themselves, there were no spoken objections at the coup. Luthor's obsession with resurrecting Brainiac, however, hurt his leadership abilities, and when he took the Legion's headquarters into space in a final bid to accomplish his goal, many of the rogues mutinied against him, led by Gorilla Grodd.
The group loyal to Grodd were Blockbuster, Shade, Hellgrammite, Copperhead, Key, Electrocutioner, Goldface, Killer Frost, Neutron, Parasite, Rampage, Silver Banshee, Fastball, Weather Wizard, Monocle, KGBeast, Lady Lunar, Doctor Cyber, Crowbar, Major Disaster, Angle Man, Bloodsport, Merlyn, and Tala.
After a battle that raged throughout the structure, Luthor sent Grodd into the vacuum of space, crushing the rebellion. With the surviving mutineers Parasite, Copperhead, Blockbuster, Weather Wizard, Rampage, Shade, Hellgrammite, Fastball, The Key, Killer Frost, and Goldface gathered before him, Luthor asked why he should spare any of them. Killer Frost suddenly defected to Luthor by freezing her comrades, earning herself a pardon. Soon after, though, Luthor resurrected not Brainiac but Darkseid (killing Tala in the process), and one of his first acts was to destroy the Hall with everybody inside.
The attack was not as successful as he thought — Sinestro and Star Sapphire managed to protect their allies with their ring and gem, although those already frozen by Killer Frost were killed. The fate of some of the Luthor supporters not shielded by Sinestro remains uncertain, including Doctor Destiny, Major Disaster, Bloodsport, Lady Lunar, the Electrocutioner, and KGBeast, (who also had switched allegiance back to Luthor). The remaining members of the Legion made it to Earth in time to warn the League of Darkseid's coming invasion. Together, they fought off Darkseid's hordes. Luthor himself confronted Darkseid with the Anti-Life Equation, resulting in them being absorbed into the Source Wall.
In the battle's aftermath, what was left of the Legion was awarded a "five-minute head start" by Batman. They were last seen fleeing from the League.
- In the Challenge of the Super Friends, one of the Super Friends animated series from the 1970s, the Legion of Doom comprised the show's main villains. The Super Friends Legion included Lex Luthor, Brainiac, Sinestro, Cheetah, Scarecrow, Grodd, Giganta, Black Manta (Devil Ray), Riddler, Toyman, Captain Cold, Solomon Grundy, and Bizarro. It was this group that inspired the Legion seen in Justice League Unlimited, down to the swamp-based lair.
- All the members of the Challenge Legion are included in the JLU version, save Brainiac (as he is in need of resurrection by Luthor), Riddler and Scarecrow (due to the Bat-embargo), and Captain Cold (who does appear during the season featuring the Legion of Doom, albeit in an unrelated episode). Black Manta appears under the name "Devil Ray", used due to copyright difficulties surrounding the Aquaman family of characters. Solomon Grundy wasn't a part of the Legion of Doom because he was killed in a previous episode. The Riddler and Scarecrow never appeared on Justice League Unlimited.
- Although the name of the Secret Society was never referred to as "The Legion of Doom", it was referred as such by the creators, and referenced by the title of the episode "I Am Legion". Matt Wayne stated that they intended to use the name "Legion of Doom" on-screen, but they were overruled by the DC Comics. Despite DC Comics' imposition, the name "Legion of Doom" is used on the package of Justice League Unlimited - Season Two (DVD).
- "I Am Legion"
- "Chaos at the Earth's Core"
- "To Another Shore"
- "Dead Reckoning"
- "The Great Brain Robbery"
- "Grudge Match"
- McDuffie, Dwayne (writer) & Dos Santos, Joaquim (director) (September 17, 2005). "I Am Legion". Justice League Unlimited. Season 2. Episode 1 (airdate). Episode 27 (production). Cartoon Network.
“ One of the nicest bits in "Alive!" was consciously making Luthor's team the villains the audience had seen most of, more or less, and cared about. Which was good, since we were hopefully making the audience worry about and root for Luthor's group. This also let us come as close as we could to the classic 13 LoD villains: Grodd was now the enemy; Captain Cold wasn't around; Devil Ray and Grundy were gone and we couldn't use Scarecrow or Riddler, so we were left with: Luthor (who kinda counts as Brainiac), Bizarro, Giganta, Cheetah, Sinestro, and Toyman (and no, I couldn't keep all 13 straight two years later without referring to my script and Wikipedia). ”
— Matt Wayne 
“ We had planned to have Flash use it as a hyperbolic way to refer to Grodd's new Secret Society in "The Great Brain Robbery". You know, "Luthor's got some kind of, I dunno, Legion of Doom" or whatever, and then we'd have the name stick. But a mid-level naysayer at DC thought the name was too corny, and that it must never be uttered. ”
— Matt Wayne