During the Incursion War, Commander Parker fought for the GDI. During or after the war, Parker suffered serious injuries which caused him to lose his eye sight. Dr. Johann Pascal gave him an optical implant but, unknown to Parker, it used Tacitus technology, connecting it to the Tiberium Control Network and Threshold 19.
The player begins his service on GST Tzadik under the command of Colonel Louise James, completing three introductory missions for her before presented with a choice by Kane. Siding with James opens up the GDI campaign, whereas siding with Kane opens the Nod campaign. Neither storyline branch was confirmed as canon.
After siding with James, Commander Parker becomes her second-in-command. Col. James assigns missions to the Commander to further determine what are Kane's plans. Eventually, the GST Tzadik is shot down by an attack made by Nod Sister Chavra and her strike team. Col. James, the Commander and their crew crashland within Tin City. Even though they succeed in escaping Nod, GDI still cooperates with Kane. James explains to General Secretary Evelyn Rios (whom she considers a traitor) and General Wesley Riggs that their "Nod ally" is using the TCN to bring back the Scrin. After been dismissed by General Riggs, Col. James declares them unfit for duty and enacts martial law.
A coup immediately follows as James orders the Fleet to head for New Adana in order to capture both Rios and Riggs. Although New Adana falls, a GDI SpecOps squad, led by General Riggs, boards the GST and captures Col. James and her officers. She is then locked away, awaiting trial. Before it comes to pass, however, the crew of the Tzadik is secretly released by Agent Duquette, with a little help from a GDI infantry squad, and sent to battle Kane at Threshold 19.
Col. James first tries a plan of her own. She shoots Kane during his speech at Threshold 19, but does not confirm the kill (it could have been a perfect replica of a double). A battle at the Scrin Tower for control of the TCN immediately follows. James' forces are victorious and she and the Commander enter the Tower. Kane addresses the Commander and shows him that Col. James knew everything about the incident that killed his wife, and had not told him the whole story. Apparently, Col. James knew that this friendly fire incident killed Lilly, but decided not to tell the Commander, so his rage against Nod would be left intact.
However, James suddenly appears and opens fire on Kane, and then shoots the Commander, fearing that his optical implant will activate the Portal. However, before the coup de grace is delivered, Kane appears once more and strangles James before stepping through the Portal, the last thing in Parker's eyes is a vision of Lilly before dying.
As the last holder of the implant, he could activate Threshold 19. The other Implants were killed by Gideon's forces, leaving Parker as Kane's only hope. Due to this, Parker undergoes surgery which made him look like Kane, though he was not willingly participating in the surgery, being surprisingly drugged before the procedure. He was then told to continue operations, and be not only Kane's eyes and ears, but to act as Kane to the public. First, he had to find Gideon's command center, and once he had done that, he captured the false prophet, parading him as a false prophet who lead Nod astray to heathen beliefs. However, despite this victory, during a speech at Threshold 19, the Commander took a shot from a sniper, nearly dying as a result. However, after a hectic battle, including a three-way match between Nod, Rogue GDI and his own forces using a stolen GDI Crawler, he was saved from death.
But the battle has only begun, and he had to fight for six TCN Control Nodes built at Threshold 19 to allow the final power-up of the Scrin tower-portal - nothing else mattered. Backed by two other Nod leaders and their Crawlers, he engaged the rogue GDI forces and emerged triumphant in the face of all impossible odds and dangerous foes - even having the guts to face the Rogue GDI leader's ace in the hole: the Arcus experimental bomber.
Within the Tower, Colonel James, mistaking Parker for Kane, arrived at Threshold 19 and shot him, inflicting him a point-blank bleeding wound. The Commander proved to be the perfect dummy, as the real Kane then showed up out of nowhere and strangled Col. James, showing her the error of her ways, while Parker awoke, giving him enough time to throw the portal of Threshold 19 open.
With his role as Ascension supporter now finished, Kane made the Ascension, abandoning the Commander and Lilly Parker, who cried over him as the Commander was dying a slow yet silent death, his destiny now come to a full circle.