Shortly after the betrayal of the Minifig/Mutant Lizard Hybrids, a important Dino Attack Outpost located near Fort Legoredo was captured by the Hybrids. At the same time, most Dino Attack agents were required to participate in an important campaign to Adventurers' Island, leaving the founding members with few options on how to retake the region. The Second Headquarters Squad was created by Specs, who decided to group together nine of the most efficient Dino Attack agents for this kind of work. The squad was named by Heavy as a reference to the original Headquarters Squad, the team of Dino Attack agents that originally established the Dino Attack Outpost in Gold City.
Upon arriving at Gold City, the Squad's first goal was to retake the Dino Attack Outpost in the region. Spy and Scout worked together to locate the outpost, then Sniper picked off the Hybrids guarding the entrance. Spy sneaked through the outpost to dispatch any Hybrids, and Scout followed and used his earpiece to report information back to the rest of the squad. Heavy, Soldier, and Demoman planned an offensive strike against the Hybrids, while Pyro, Medic, and Engineer located Gold City's abandoned mine to gather resources.
In the following days, the Dino Attack Outpost was retaken by Second Headquarters Squad. With the resources gathered at the mine, Engineer built sentries and defenses to protect their base. With Engineer and Sniper staying behind to guard the outpost, the rest of the squad launched their major offensive attack. They were met with surprising success and cleared a third of Gold City from the threat of Mutant Dinos and Hybrids. Most of Second Headquarters Squad celebrated this success in a nearby tavern, despite Spy's warning that this was merely the calm before the storm.
With the help of Engineer's building skills, the Second Headquarters Squad converted several key points in their section of Gold City into control points. Unfortunately, as it turned out, Spy's suspicions were correct. The Hybrids struck back in full force, driving the Second Headquarters Squad back. In the following days, the Hybrids captured control point after control point, pushing the Squad back until, at last, once again Gold City was entirely under Hybrid control. Currently, the Second Headquarters Squad is desperately trying to defend their last control point: the Dino Attack Outpost.
Hybrids laid siege upon the Dino Attack Outpost, but the combined might of the Second Headquarters Squad created a nearly-unbreakable defense. In an attempt to lessen the Hybrids' numbers, Heavy charged forward with Medic at his side. The two Dino Attack agents were a nearly invincible team, with Heavy shooting down any Hybrid foolish enough to approach and Medic quickly patching up any wound. They made it as far as the first control point, where Heavy decimated the Hybrid squad there. However, Heavy and Medic were forced to make a sudden retreat when Heavy's machine gun unexpectedly ran out of ammo.
Second Headquarters Squad later made a stunning revelation: the Hybrids had taken over Fort Legoredo and were using it as their main base of operations. In response, the squad found an old mining track leading to the fort and assembled a bomb cart, which they intend to use to blow up the fort. However, since Fort Legoredo is such an important location to the region's history, the squad first requested permission to blow up the fort, and Specs apparently approved the decision.
Clint Wayne, Angel Eyes, Maria, Harmonica, and Firecracker later joined up with the Second Headquarters Squad. Disapproving of the team's decision to bomb Fort Legoredo, they have decided to take matters into their own hands. However, after the group infiltrated Fort Legoredo and lowered the Hybrids' defenses, the Second Headquarters Squad went ahead with their plan to send the bomb cart to Fort Legoredo. As Clint Wayne's posse, Spy, Heavy, and Medic took care of the Hybrids' defenses, the bomb cart was free to reach Fort Legoredo and destroy the fortress, killing all the Hybrids inside and resulting in a Dino Attack victory.
The Second Headquarters Squad has returned to Dino Attack Headquarters to celebrate their success. However, during their celebration, Engineer was killed by XERRD's mole, prompting an investigation into the identity of the mole. In the following hours, the majority of Second Headquarters Squad was killed in their attempts to identify the mole, leaving only Pyro and Demoman as survivors.
The Second Headquarters Squad is officially considered disbanded. Its two surviving members, Pyro and Demoman, have banded together with a group of other Dino Attack agents to form the Third Headquarters Squad.
- Soldier, who specialized in military combat. He was also the squad's self-proclaimed leader.
- Pyro, who specializes in pyrotechnics.
- Demoman, who specializes in explosives.
- Heavy, who specialized in heavy weaponry.
- Scout, who specialized in reconnaissance.
- The Second Headquarters Squad is heavily inspired by the multiplayer first-person shooter game Team Fortress 2. The squad's members are based upon each of the nine character classes, and Second Headquarters Squad itself is named after Team Fortress 2.
- Second Headquarters Squad was created so that it would one day serve an important role in determining the identity of XERRD's mole in Dino Attack Team. This role involved the majority of the squad being killed off by the mole in a sequence of events heavily inspired by the "Meet the Spy" promotional video for Team Fortress 2, while Rex survives with the knowledge of the mole's identity.