Zackaria led the Imperial Senate's forces in The Battle for Kethlan. His original intention was to capture Minotaur, whilst eliminating the remainder of the Emperor's forces. However, when the battleship was destroyed, Zackaria masterminded the theft of Dragon.

Following the fall out of Operation Menelaus, Zackaria met with Anthony Hawke, intending on using Ifrit to trick Griffin into believing that a rescue party had arrived at the Phylent system to assist them. In the battle that ensued Zackaria was spaced from the bridge of CSN Ifrit when Simon Dodds attacked it.

Though he was exposed to the vacuum of space, Zackaria apparently survived the attack and now holds a grudge against Simon Dodds. He was rescued by transport shuttles that departed CSN Ifrit and fled with Dragon and the remainder of the Imperial forces.

Jason Zackaria joined the invasion of Mythos after learning about Ifrit being shot down and the White Knights being amongst the evacuees. He found Simon Dodds in the north of New Malaga, as the pilot was trying to free himself from an overturned Sabretooth and escape the fighting.

Zackaria felt extreme anger towards Simon Dodds when he found him, having held a grudge against him since the pilot had spaced him during the battle in Phylent. He considered that Dodds had humbled him before his troops and had decided against forcing Dodds to join the Mission, intending on killing him there and then, instead. He was prevented from doing so when a bomb strike on the plaza caused his bodyguards to evacuate him from the area.

He gave Julian Rissard a dressing down after discovering that he had tortured and beaten Kelly Taylor and Enrique Todd, dismissing him from the task of guarding the two. He ordered for Enrique to be given medical attention and then had the two pilots fed and allowed to relieve themselves.

He fled the Coyote system when the facility that Enrique and Kelly were being held at was attacked, ordering in a nuclear strike on the planet shortly thereafter.

Zackaria's encounter with Simon Dodds was significant as he was the only person outside of the Pandoran army that Zackaria had spoken to in a number of years. Kelly Taylor attempted to address him when he came to her cell, but the man largely ignored her.

Zackaria continued to lead the frontline Pandoran fleet as it pushed out from Imperial space, following the initial invasion of the Independent worlds. He continued his taunts of the CSN and allied forces during that time, naming Dodds in some of his speeches.

As the Pandoran fleet closed in on the inner Helios systems, Zackaria began returning to Imperial space, in search of the Senate and his instructions for the conclusion of the war. He was unable to locate either the Senate or the Senior Magistrate, unaware that they had been killed many years before.

In late 2624, Zackaria was met by Simon Dodds on Kethlan. Dodds begged Zackaria to end the war and not to destroy Earth, but Zackaria refused to hear him out. Chaz Koonan and Enrique Todd both attempted to speak to him, but Zackaria ignored them, only interested in speaking to Dodds. He sneezed as the four spoke, proving that he was suffering the ill effects of the nanomachines breaking down, though the action passed the three men by. Eventually Chaz spoke to Zackaria through Dodds, telling him of what had happened to the galaxy and how he had been tricked. Though Zackaria was for a time convinced and began to overcome the control of the nanomachines, a group of malfunctioning Pandoran soldiers interrupted the dialogue, causing Zackaria to retreat and label Dodds "Judas".

In the final battle for the Solar System, Zackaria took to the field in an Imperial Sphinx. He attacked Dodds' ATAF several times before chasing the pilot on to one of Dragon's flight decks. He pursued Dodds through the battleship, attempting to stab him with the Imperial navy's ceremonial dagger. His health failed him a number of times along the way and Dodds was able to easily overcome him in hand to hand combat. Despite his failing health, Zackaria managed to stab Dodds in the shoulder. He chased Dodds out of Dragon as the pilot escaped after arming the bomb.

Though he escaped the detonation zone of the TSB, Zackaria's Sphinx was heavily damaged by the bomblet explosions that followed Dragon's destruction and ended up crashing down in Earth Orbital One's central garden. Zackaria crawled from the wreckage of the Sphinx and regained control of himself as he lay dying. Dodds found and questioned him, Zackaria wanting to know whether or not the Pandoran fleet had been defeated and the allies had won. He apologised to Dodds for everything that he had done over the years and told Dodds of how he was nothing but a prisoner in his own body. He finally recognised Chaz and apologised for not being able to enjoy the celebratory drink with him.

Before he died, Zackaria asked Dodds whether or not he would be able to forgive him. Dodds said that he would be able to quite easily, though Zackaria did not hear him.