G-Nome casts the player into the shoes of Sergeant Joshua Gant, a retired Union Intelligence Agency operative who has been out of action since a disastrous mission took place ten years prior in 2215 A.D., in which his closest friend, Ron Pearl, was lost and presumed dead, due to the fiendish negligence of the unscrupulous Major Jack Sheridan. Now, in 2225 A.D. a mineral-rich Phygos star system has been discovered at a critical location within the Milky Way, causing the tactical mobilization of the Darken Republic, Bendian Mercenaries, the Union and the Scorp Empire, the greatest adversaries known to man. The U.I.A. have recently uncovered a biological weapons program developed by the Scorp Science Corp., which involves modifications of the human genome, which has bread a new, incredibly dangerous monster known only as the "G-Nome". The most controversial and horrendous fact of the matter is that there are indicators that human P.O.W.s have been used as test subjects for the experiments, an accute violation of virtually every weapons treaty between the Union and the Scorp. Therefore, Gant is reinstated as an undercover operative, with the objective of partaking in a solo land-based mission that is only viable if it begins on the outskirts of the Darken frontier.
The mission commences and after a brief skirmish with a small Bendian raiding party, Gant infiltrates the Darken Republic. He is informed that his former squad member and friend, Stephen Kylie, has left coded messages across the Darken territory and that he is awaiting Gant near Chambers Pass, located at the Darken-Merc frontier. After having his stolen Darken Sentry HAWC confiscated by the border control agent Commander Alm'sh Kor, Gant slips in with her convoy en route to the regional headquarters, where he learns that he must acquire Kylie's radio signal from the regional LATLON Communitcations Array. Gant's first major combat experience occurs at the array, where he is forced to destroy the entirety of the Darken defenders and after learning that Kylie is nearly out of time, due to a blown cover, he destroys the Darken's communications altogether. With their communications disabled, Gant fights through the Chambers Pass border guard and meets up with Kylie.
Finally in Merc territory, Gant and Kylie attempt to receive a dropship rendezous package that includes two Union HAWCs, but due to a leak, the dropship crew is destroyed and the Mercs steal the vehicles. After destroying the vehicles intended for them and receiving replacements, the duo determine that their next squad recruit, genetic scientist Doctor Victoria Thane is in danger. Gant and Kylie move quickly to destroy the Merc's LATLON Communications Array and after an intense battle with a large Merc raiding party, they rendezous with Thane. The Doctor is informed by U.I.A. Director General Allance Wilkins of the G-Nome situation. Thane concludes that the method to destroy the creature would be to obtain a neural inhibitor from the Merc compound that houses a citadel atop Mesa Caracon. The team resupplies with Merc vehicles and make their way to the base of the mesa, from where they take an elevator to the top, where they infiltrate the facility. The Mercs become aware of this infiltration, however, and dispatch a wave of attack fighters to eliminate the Union combatants. After a short battle, Thane obtains the needed materials and the group escapes into Scorp territory.
Near the Scorp frontier, the Union agents find that the border crossing is heavily defended and the only realistic way to proceed would be to join a recon convoy, using stolen indentifier codes. This plan produces terrible results, however, as the convoy is confronted by an off-course Union patrol. Disgracefully, Gant is forced to assist in the elimination of his comrades. Once inland, General Wilkins informs the team that their final squad member is none other than Sheridan, who is the Union's single-greatest expert on Scorp culture and technology. Sheridan directs an assault on the Scorp's LATLON array at Ur-Kinsk, which allows for the team to assault the weapons depot of Ur-Ulit, in order to obtain Scorp vehicles that have imaging technology to uncover mine fields. Once the vehicles are obtained, the team assaults Ur-Alr, which has a headquarters that contains the secretive files that direct to the G-Nome laboratory itself. The team defeats the Scorp Elite Peacekeepers and arrive at the facility and after Gant destroys it, Sheridan shows his true colors by attempting to kill Gant and capturing the G-Nome. Kylie is captured by the Scorp and held at the regional headquarters, where Gant and Thane attempt to rescue him, but they themselves are captured by the Scorp Directorate Prees Tak. Unexpectedly, Tak agrees to team up with the U.I.A. and fight Sheridan's forces that attempt to destroy Ur-Kinsk. Despite eliminating the sizable army, they discover that it was simply a diversion for Sheridan's main column to escape into the volcanic Shalton frontier, where Sheridan's alleged recombination lab is hidden.
The Scorp see Gant and his team off. After encountering multiple Darken and Merc firefights, the team allow for reinforcements, including General Wilkins, to arrive and assault Sheridan's heavily-defended lair. Satelite imaging, however, indicates that Sheridan is making an attempt to transport D.N.A. samples off-planet and their time is short. In command of the highly sought-after Union Heavy Assault HAWC, Gant fights through Sheridan's forces alongside Kylie and destroys the lab. As the remaining renegades are taken care of, however, Sheridan personally kills Kylie and attempts to flee with the G-Nome. With a vengeance, Gant gives chase and after one-on-one combat, kills the traitor. Picking up the neural inhibitor device from Sheridan's corpse, Gant approaches the battered cargo bay that holds the G-Nome and makes his stand. The creature attacks Gant, but is quickly neutralized by two shots from Gant's weapon. About to kill the creature, Gant notices a bar code on the G-Nome's paw and looks closer to see that it reads "R. PEARL". In shock, Gant contacts Wilkins and hesitantly informs his superior that not only Sheridan was dead, but the G-Nome was killed. As the creature awoke, Gant yelled at Pearl to escape. The last image seen is of the G-Nome walking into the sunset.
Following the G-Nome's escape, Union agents swarm and inspect Sheridan's lab and look for remains of the G-Nome in the area, to no avail. Wilkins, however, is transfixed upon a pitri dish amongst the remains, which reads "G-NOME: PEARL". As the Union forces begin to move out, Wilkins snatches up the dish and disappears. Soon after, the Scorp Imperial Tribune declare war of the Union, in response to the disastrous infiltration of their territory. Public knowledge of the mission is minimal; the only indication of its existence is the unexpected resignation of Wilkins. Botht the Union and the Scorp deny the mission, despite the repercussions of war.