In early 2617, the Pandorans intercepted Dragon in jump and hijacked it, slaughtering the crew but sparing Anthony Hawke, the acting captain. In June of the same year they engaged allied CSN and UNF forces in the Aster system, where they made short work of their adversaries.

During the incident at Arlos starport, several of the soldiers demonstrated a strong resilience to gunshot wounds, as well as strength and fighting advantages over their opponents.

They follow the orders of Jason Zackaria to the letter and put his safety above all else, as they demonstrated when the admiral was spaced from Ifrit's bridge. The group immediately ceased their attack on Griffin and the White Knights, for fear that a stray shot might strike him.

Towards the end of 2617, the Pandoran army had commenced its push beyond the Mitikas Empire, striking a number of boarding independent star systems, including Coyote. Once again lead by Jason Zackaria, the army succeeded in tracking Ifrit through jump, intercepting the vessel and forcing it back to normal space. Originally intending on taking command of the ship, they were thwarted by Christopher Hail, the captain, who ditched it in the Tanis Sea on Mythos.

During the invasion of Coyote, the soldiers once again displayed superhuman feats, as well as showing no mercy towards their opponents, once more repeating the mantra of taking no prisoners and sparing no lives. They did, however, make two exceptions to this rule: capturing Kelly Taylor and Enrique Todd and leaving Simon Dodds to the mercy of Jason Zackaria.

It was revealed to Estelle de Winter by Edie Thompson that the Pandoran soldiers were in fact citizens of Mitikas, who had been infected by specifically-crafted nanomachines, created by the Imperial Senate (hence, The Senate's Mistake). Having spent a considerable amount of time in Mitikas during the initial uprising of the Pandoran forces, Chaz Koonan was already quite aware of the threat they posed to the galaxy, as well as their strengths and abilities. His own personal situation, however, forced him to remain tight-lipped about the matter, until the Helios Confederation could formulate a plan of action for dealing with them.

Later, Natalia Grace confirmed that the Senate had created the nanobots in response to their ongoing war against the Crown Emperor Adam Lorenzo III. The bots not only granted their hosts superhuman abilities (such as advanced healing, strength, reactions and a hive mind), but also made them completely loyal to the original Senate and to their cause (The Mission).

Their original instructions had been to eliminate all opposition to the rule of the Imperial Senate. However, these instructions were so broad in depth that when the original senate were killed during the war, the infected were left with no one to order them to stop after they had sacked Kethlan and taken the Seat of the Emperor. They therefore opted to continue carrying out these instructions, seeing the Mission as incomplete. They subsequently turned their attentions to the independent worlds and the Helios Confederation.

As of the end of 2617, the strength of the Pandoran army was approximately 20 billion soldiers. In response to the extreme danger of entering into an unwinnable war against the Pandoran Army, the independent worlds and Confederation launched Operation Sudarberg. The operation failed.

Between late 2617 and late 2624, the Pandoran army stepped up its campaign against the Independent worlds and the Helios confederation. The assaults against the Independent worlds involved both ground attacks, orbital bombardments, and, once all resources had been looted from the target planets and systems, nuclear strikes. They continued to add to their hardware as they progressed through the galaxy, though they did not recruit any more members.

Other clothing styles emerged around 2620, as materials used to create the signature black suits ran out, and the Pandorans soon appeared clothed in the uniforms and armour of regional Imperial troopers. The Enemy continued to hijack and acquire vessels during the Mission, using the ships to transport their numbers out of Mitikas and to the frontline.

While attacking Alba, the Pandorans misfired Dragon's anti-matter cannon, striking Torelli and causing a firestorm to commence. The attack was not intentional, however after this the Pandorans began using the anti-matter cannon more frequently, increasing the pace of their campaign by leaps and bounds.

In November 2621, after successfully sacking the Independent nations, they attacked Helios, via Temper, falling into a trap laid out by the allied forces, known as Black Widow. Around one-fifth of the Pandoran army (and ninety percent of those that jumped into Helios) were destroyed in the ambush. The Pandorans had actually anticipated the attack and ended up luring the allied forces into a trap of their own, in the Adetton system. After smashing the allied forces and routing their forces, the Pandorans returned to Temper and destroyed Spirit.

Starting around 2623, the nanomachines that controlled the Pandoran soldiers began to break down and malfunction. Ultimately, the replication process employed by the nanomachines was at fault and the nanobots themselves started to mutate. Unable to perform their tasks properly, the machines attacked the host directly, including their very DNA, causing the men and women they were controlling to effectively develop cancer.

The cancer caused side effects such as dementia in the soldiers and their abilities and skills suffered. Their strength, healing abilities and skills deteriorated, to the point where they were unable to recognise threats. Simon Dodds was among the first to recognise that the soldiers were dead and dying, when Griffin arrived in the Kethlan system. On the planet Kethlan itself, the soldiers there were found to be fighting one another, unable to tell friend from foe.

Though dying, the Pandorans continued to prove formidable opponents and tested the allies greatly, even in the final battle for the Solar System. Upon Zackaria's death and the destruction of Dragon, the Pandorans retreated from Sol and returned to Mitikas, to await new instructions. In the two year mop-up operation carried out by the allied forces, many of the Pandorans were discovered to have died of the nanobot malfunctions, and those that remained alive presented little opposition.

The last confirmed active soldier was shot dead in Turl, a city on Hyanik, in 2627.