In 2008, years after the last appearance of Evil Ogel, the LEGOLAND government felt that the Alpha Team was no longer needed. As a new threat, Dr. Inferno, rose to power, the LEGOLAND government began funding the creation of a new organization of secret agents intended to replace the Alpha Team and deal with Dr. Inferno. Alpha Team was not pleased with this decision, and an inter-agency rivalry was formed between the two organizations.
The Agents Defense Organization spent most of their resources on infiltrating Dr. Inferno's bases and foiling his schemes. However, they occasionally conflicted with Alpha Team as well. Attempts to ameliorate relations between the teams resulted in Alpha Team agent Frozeen strangling Agents representative Grease, embittering both teams. In one instance, Agents actually fought alongside Ogel's forces when they learned of an alliance between Alpha Team and Dr. Inferno.
The Agents worked quickly to foil Dr. Inferno's master plan. Agent Chase pursued Saw-Fist with a jetpack and retrieved a stolen energy crystal while Agent Charge raided Break Jaw's secret swamp base. While Charge pursued Gold Tooth's high-speed attack jet in the Agents supersonic jet, Chase rescued Agent Trace from the clutches of Break Jaw before infiltrating Dr. Inferno's base and stealing his laptop, revealing Dr. Inferno's plans to build a giant laser cannon.
Dr. Inferno was captured and held prisoner in the Agents Mobile Command Center, but was broken free by the efforts of Spy Clops and Gold Tooth. Charge and Chase teamed up for an undersea mission to stop Break Jaw for good, and then the full Agents team attacked Dr. Inferno's Volcano Base, rescuing Agent Fuse and foiling Dr. Inferno's master plan.
After the defeat of Dr. Inferno, the Agents Defense Organization approval ratings skyrocketed, and more funding was given to the Agents, allowing for an upgrade in technology and an increase in recruits. The new and improved Agents Defense Organization was often promoted as Agents 2.0 to the public.
In 2009, Dr. Inferno appeared to have resigned from his plans to take over the world, but Agent Chase refused to let his guard down as the mad scientist launched a Tiny Turbos Championship. The Agents were dispatched across LEGO City to stop crimes committed by Dr. Inferno's associates and henchmen, including Magma Commander and Dr. D. Zaster.
Eventually, Dr. Inferno revealed his new evil plan to attack LEGO City in his towering robot mech. He terrorized the citizens of LEGO City, and the full forces of the Agents Defense Organization were dispatched to take down the robot before it caused too much damage. They were successful and once again foiled Dr. Inferno's plans.
In 2010, the Mutant Dinosaurs appeared all over the LEGO Planet, leaving chaos and destruction in their wake. While Alpha Team had its hands full in relocating the world's populations to hastily-constructed refugee facilities in Antarctica, the Agents Defense Organization boasted that it could handle the Mutant Dino threat. Nonetheless, Alpha Team succeeded in convincing the LEGOLAND government to instead fund a new organization created specifically for stopping the dinosaurs: Dino Attack Team. As such, while Dino Attack and Alpha Team had a positive relationship, the inter-agency relations between Dino Attack and Agents were bitter at best.
Eventually, Agents Defense Organization learned that the Green Goo of the Goo Caverns provided a potential weapon against Mutant Dinosaurs, and so Agents were dispatched to the underground tunnels to take control of the area. By the time they arrived, however, Dino Attack Team and Evil Ogel were already mining the substance, and after a bitter conflict of interests the Agents agreed to let Dino Attack Team handle the underground operations.
However, the Agents attempted to arrest two civilians working with the Dino Attack Team for being in a restricted area: Kat and David Norman. Alpha Team and Dino Attack Team had to pardon these figures to get them free, creating further disputes between the organizations.
Arguments arose at an Antarctic Agents outpost where they caught several Dino Attack agents and allies on a secret mission. The confrontation was eased due to Captain Osprey, who suggested that the Agents and Dino Attack get over their petty rivalries and work together against the common threat of Mutant Dinos. From this point on, relations have gotten better between the two organizations.
The main Agents Headquarters is located in an undisclosed location of the LEGO Planet, but a smaller base of operations exists in LEGO City, from which mission briefings are held and top-priority prisoners are held in a high-security cell. The Agents also use the Mobile Command Center as a mobile headquarters.
- Chase: The leader of the Agents.
- Cloudchaser: A member of Colonel Dashworthy's jet fleet. She was killed in the battle against the Witch's Windship.
- Covert: A colonel in the Agents Intelligence Division who frequently clashes with Magma.
- Cyrus: A pilot who was Stromling before the Maelstrom Temple was cleansed. He was killed by Loop.
- Desdemona: A helicopter pilot who flew with Osprey and Jinx during the final battle in LEGO City.
- Epic Winston: Real name Winston Grendelwulf, a lieutenant who uses a massive broadsword to cut throw foes. He willingly succumbed to his battle wounds and died after the final battle.
- Francis: A technician who aided Thaddeus Brickhouse on Adventurers' Island. He was killed by Wheatley.
- Gilda: A member of Colonel Dashworthy's jet fleet. Gilda was killed by Willa the Witch's Maelstrom orb.
- Grease: A high-ranking Agent who is infamous for his snobby attitude.
- Hazmatt: Real name Matthias Grendelwulf, a lieutenant who drives a custom ADO motorcycle with his brother. He was killed by Sargon.
- Hugh Yena: A corporal who assisted Dino Attack Team during the search for ShadowTech Island and the battle for the Temple of Hotep III.
- Jesse Obvious: A captain who participated in the final battle in LEGO City.
- Jinx: A lieutenant who flew with Osprey and Desdemona during the final battle in LEGO City.
- Nightmare: A member of Colonel Dashworthy's jet fleet. Her jet is painted solid black.
- Osprey: A captain who seeks positive relations with other organizations.
- Phoenix: A pilot who was a Stromling before the Maelstrom Temple was cleansed. She was killed by Loop.
- Raine Dashworthy: A confident pilot who flew a supersonic jet during the final battle. She was promoted to colonel after Score was killed.
- Rapidfire: A member of Colonel Dashworthy's jet fleet. He sacrificed himself in the battle against the Witch's Windship.
- Score: A colonel and one of the Agents' commanding jet pilots. He was killed by Dr. Rex during the final battle.
- Snaproll: A pilot assigned to fly prisoners to headquarters for interrogation. He was murdered by Cane.
- Snowflake: A member of Colonel Dashworthy's jet fleet. Snowflake was killed in the battle against the Witch's Windship.
- Soarin: A member of Colonel Dashworthy's jet fleet. Soarin was killed in the battle against the Witch's Windship.
- Spitfire: A member of Colonel Dashworthy's jet fleet. He was killed in the battle against the Witch's Windship.
- Thaddeus Brickhouse: An older captain who pilots an Aerial Defense Unit. He was killed when his helicopter was shot down by Blaire Darkling.
- Wheatley: An Agent who was later corrupted into a Stromling and attempted to hijack an Aerial Defense Unit. He was killed by Thaddeus Brickhouse.
- Zachary Virchaus: A young agent who joined shortly after the Dino Attack began. Resigned later on to join the Dino Attack Team.
- Although initially depicted as overly snobby and rude in Dino Attack RPG and Alpha Team RPG: Ogel's Last Stand, it was once mentioned that, since the RPGs are told through the eyes of the Dino Attack Team and the Alpha Team respectively, in their eyes the Agents appear to be more antagonistic than they really are. As Dino Attack Team's relationship with the Agents improved, they were progressively depicted in a better light over the course of the RPG.