Mere days afterward, Nod and GDI forces would, ironically be forced to team up in the Firestorm Conflict when CABAL went rogue. With Kane, Cairo and Sarajevo, the Banshee factories, and much of their missile-based arsenal lost, Slavik had no choice but to go underground. However, after Kane's defeat at Cairo, he was forced to retreat with the other Nod leaders from GDI's view. After retrieving the Tacitus, Nod forces captured the mutant Umagon and destroyed a number of GDI research facilities, as well as delaying the deployment of the Mammoth Mk. Kane, however, tasked Slavik with recovering the Tacitus, an alien database that was on board the ship Vega crashed. With Nod reunited, Kane initiated several assaults on GDI bases around the globe. Coincidentally, Kane also revealed himself to the Brotherhood at this time, which had the effect of uniting the fractured segments of the Brotherhood of Nod. Linking up with Nod forces loyal to Kane, he successfully deposed Hassan as the de facto leader of the Brotherhood. The events of the Second Tiberium War eventually culminated in McNeil defeating Kane (and Nod) at Nod's Cairo missile launch facility, narrowly averting a chemical missile launch and the destruction of the Philadelphia.ДЄnton Slavik, a Black Hand prelate and experienced commander, managed to escape a Nod holding facility under the command of the GDI's puppet leader Hassan. He discovered Nod was also attempting to set up ICBM launchers to target and destroy the Philadelphia. While en route to Egypt, McNeil's command ship was grounded by an ion storm however, after holding off Nod forces, he continued uninterrupted. Disobeying orders from General Solomon, McNeil left immediately. In the middle of these operations, the mutant Umagon was captured by Nod and taken to Kane's pyramid in Cairo to complete her Divination. For GDI to successfully conclude operations in Europe, both of these threats were to be dealt with. General Solomon, then contacted McNeil about Kane's new chemical missile facilities and Banshee fighter factories. In the process, McNeil's brother, on station in Hammerfest, was killed by Nod forces. Commander McNeil led an amphibious assault group into the base, evicted the occupying Nod force, and retrieved the sonic crystals being held in the base from Slavik's forces.

The speculation about the alien ship was quickly put on hold, as Nod forces under the command of Anton Slavik attacked and captured GDI's fortress in Hammerfest, Norway. McNeil successfully captured Vega's stronghold and attempted to interrogate Vega, however, Vega's drug-induced insanity and Kane launching a nuclear strike on the facility prevented McNeil from getting anything more than cryptic hints about the origin of the alien warship. Upon rescuing Tratos, Solomon sent McNeil to South America to assault General Vega's stronghold. He did, however, encounter a Forgotten mutant by the name of Umagon, who promised the support of her Forgotten comrades in return for GDI support in rescuing their leader, Tratos. From the Phoenix base, however, McNeil attempted to and did secure an alien warship Nod's General Vega crash landed, although he was unable to secure any significant hardware. Although he succeeded in driving Nod from the region, GDI suffered heavy losses. GDI's Commander McNeil was initially deployed to stop a Nod task force attacking GDI's outpost in Phoenix, AZ. These events marked the beginning of the Second Tiberium War. Immediately after, Kane initiated combat operations on a number of GDI positions and contacted General James Solomon, aboard the GDSS Philadelphia. Slavik, who saw Hassan as a traitor to Kane, overthrew Hassan's leadership, while Kane simultaneously revealed himself to the Brotherhood. GDI, however, mitigated Nod's effectiveness by installing a puppet leader ( Hassan) over the largest splinter faction of Nod. This 'disappearance' made Kane immortal in the eyes of some of the Brotherhood, which allowed Nod forces to continue operating even thirty years later. Despite winning the First Tiberium War with the Ion Cannon strike on the Sarajevo Temple complex, GDI forces were unable to account for the body of Kane a singular fact that the GDI High Council later saw as a costly oversight. Tiberian Sun follows Michael McNeil (GDI) and Anton Slavik (Nod) as they command Global Defense Initiative and Brotherhood of Nod forces during the Second Tiberium War.

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