Exofleet had been informed by Marduk, an Exofleet spy, that a garganturan underground complex was located on Mars. Barca, a Neosapien spy, had alerted Typhonus to the operation. After entering Mars's orbit the the E-frame squads were ambushed by a Neosapien force that had a 5-to-1 advantage. DeSoto ordered a withdrawal, but 50% of the Exofleet E-frames had been destroyed. Able Squad had gone to the surface of Mars to create a diversion for the other squads.

On the Cobra, Marsh was telling DeSoto that the operation had been compromised when the Avenger exploded. Barca then seized control of the Cobra and imprisoned the Exofleet personnel. Barca revealed to Marsh that Phaeton had promised him Venus in exchange for sabotaging Exofleet. Barca met Typhonus and told him that he would deliver a Neosapien monitor to Winfield. The monitor had been laden with explosives, similiar to a fire ship or the hellburners. Once in range, the monitor would explode and destroy the Resolute II. With the flagship destroyed, Typhonus would be able to decimate the remaining Exofleet ships.

Barca told Winfield that the ambush had destroyed the Exofleet squads, but they did manage to capture a monitor. Barca ordered the remaining Exofleet personnel transfered to the monitor. The Mars Fleet waited just outside Exofleet's sensor range for the Resolute II to be destroyed. Hallas had become dis-illusioned with Barca and freed Nara Burns. Burns and Hallas escaped, damaging the Cobra's sensor systems with a Chain Lightning attack. This meant that Barca did not know that the tractor beam had also reactivated. Able Squad escaped the monitor, but the Cobra was destroyed. Informed that the operation had failed, Typhonus ordered the Mars Fleet to retreat.

Later, the initial mission to investigate the unknown underground complex was re-activated since Exofleet had to know its function. Unknown to them, Marduk had been captured. Able Squad landed on Mars and Marsh told them about the mission. Able Squad was attacked by a patrol, when informed of this Marsh canceled the mission since they had lost the element of surprise. As the squad prepared to leave Mars, Marsh was ordered to extract Marduk since he had the locations of the Mars Defense Systems.

At the Falls of Eris, Marduk revealed the trap; but numerous Neosapien E-frames appeared and overwhelmed the Exofleet squads with superior numbers. Alec DeLeon used the Mega Burst Jamming Device to devastate the pursuit units. Marsh informed Winfield of the trap and the severe casualities that had been taken. Baker Squad was nearly destroyed.

Able and Baker Squads arrived at the site of the underground complex, Marsala believed that it had not been constructed by the Terrans or the Neosapiens. Marsh decided to enter the structure. Typhonus had found Marduk's computer files and ordered that a search party be sent to investigate. When Marsh relayed the discovery to Exofleet, he was contacted by Algernon onboard the Arnhem. While resistant to the diversion, Butler agreed after being told that alien technology would provide a definitive technology edge.

The initial attempt to breach the structure met with failure, but the explosion was detected by the incoming Neosapien unit. A firefight began, but the Exofleet squads were outnumbered and forced to retreat into the structure. Typhonus's breaching explosive charge worked and the explosion was detected by the Exofleet squads. Inside the structure, the Exofleet squads were attacked by the defense systems. When the Neosapiens arrived, the defense system attacked them as well.

The Arnhem had arrived, but Butler was only using 1 fireteam since the situatation was an unknown factor. Furthermore, Butler was going to cancel the mission since contact had been lost with Marsh. Just then, the structure raised a spire that had been activated by the firefight inside. Butler decided to land and ordered the shuttle prepared for an evacuation. The Neosapiens managed to exit the structure, Typhonus called for reinforcements.

The Jumptroops landed and were attacked, the spire's interference prevented him from summoning the rest of Charlie Company. Able squad used a Fusion Pack explosion to exit structure. Once outside they provided air support for the jumptroops. The spire began emitting energy waves, Algernon then realized that the spire was a radio transmitter.

The energy waves overloaded the E-frame's electrical systems and both sides were making ineffective repair attempts. Vince Pellegrino realized that Typhonus and his troops were outgunned since the lighter jumptroop E-frames were operational, Butler approved of the idea and led an assault. After losing several E-frames, Typhonus retreated to the gullies. Since the heavier E-frames were needed for that type of terrain, Butler left several jumptroops to maintain a forward line.

For an unknown reason, the E-frames regained power. Butler wanted Marsh to destroy the Neosapien positions, but Marsh refused since the unknown structure more important to Exofleet. Butler recalled the jumptroops. Algernon explained that the transmitter could prove to be the most powerful weapon in the solar system. Exofleet needed to discover the power source. Despite his losses, Typhonus decide to counterattack, but Phaeton ordered him to discover the source of the spire's power.

Able Squad entered entered the structure while the jumptroops remained outside. The Neosapiens also entered the structure. Able Squad entered the central chamber and were soon attacked by Typhonus. The final 2 members of Baker Squad were killed by the defense system. Kaz Takagi had lost control of his E-frame because of Typhonus's remote control override. Takagi escaped and the E-frame was propelled into the energy generator.

This caused the Fusion Pack to explode. The generator was destabilized and began a self-destruct sequence. Both sides began to evacuate the structure. Butler called for the Arnhem's shuttle after the spire fired an energy beam and marsquakes began. Energy beams then appeared all over Mars. Inside the structure, multiple explosions were taking place.

The shuttle arrived and Butler said he was going to leave as soon as the structure showed external explosions. Inside, Typhonus was the only survivor of the energy wave, which destroyed the other Neosapien E-frames. Able Squad exited just as Butler was ordering the shuttle to leave. Typhonus managed to escape, but Rita Torres stole his shuttle and left him on the surface.

More explosions occured, locations such as Maginus City were destroyed by lava and magma flows. Finally, the entire planet exploded. Phaeton was enraged by the destruction of Mars and made the first mention of the Doomsday Device. Torres reunited with Able Squad and they returned to Venus.