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The story begins with the UNSC's early battles on Harvest, but also features another colony world, Arcadia, which holds "something of great interest to the Covenant." The planet is subsequently invaded by the Covenant and the UNSC must evacuate the planet while engaging the invasion force. The Flood is significant in the storyline and several massive Forerunner structures are also explored.

The Spirit of Fire is "full of new characters," such as the AI Serina, Professor Ellen Anders, Sergeant John Forge, and the Spirit of Fire's commander, Captain Cutter. Some of these characters go planetside to aid the player.

While Sergeant Forge is patrolling the northern regions, Alpha Base was attacked and destroyed by the Covenant, with survivors fleeing to the countryside surrounding the area. Rounding up these survivors, Forge leads them in an assault that removed the Covenant presence and reestablished Alpha Base, returning it to operational status. Forge leads an assault on the relic site itself, removing the Covenant occupiers and preventing the enemy from destroying it to deny human access, and securing the site for Anders to examine it briefly before a Covenant counter-attack cuts them off from Alpha Base. Grizzly tanks launched from the Spirit of Fire manage to cut through the Covenant, linking up with Forge and his Marines, and escorting them back out through the relic while forces from Alpha Base held off the Covenant. Information gathered from the Harvest relic shows that the Covenant have been pointed to a second UEG colony, Arcadia.

Following the Covenant to Arcadia, they find that the most of the orbital defense ships have been either destroyed or damaged in battle with the Covenant (one of the many ships is the UNSC Pillar of Autumn which would be involved in the "Halo incident" twenty years later). Sgt. Forge and his forces deploy on the ground in order to assist the SPARTANs from Red Team in the effort to evacuate civilians from Arcadia City, via cargo transports. Afterward, the UNSC forces withdraw to a defensible area on the city outskirts, holding off Covenant attacks long enough for SPARTAN Group Omega to arrive and assist in the destruction of local Covenant forces. At the same time, the Covenant have erected a large energy shield generator around a site of importance, with undiscovered ruins surrounding the area, forcing the UNSC to deploy prototype Rhino plasma artillery to penetrate it. Moving in to examine what was of such interest to the Covenant, they come under attack from a Super Scarab, only partially complete and annihilating any UNSC forces in its line of sight. Eventually managing to destroy it, Anders and Forge begin documenting the area, only for the Arbiter to arrive, taking Anders prisoner and wounding Sergeant Forge, with Red Team arriving too late to assist. Rapidly heading out of the system aboard a starship, the Spirit of Fire follows, eventually emerging in orbit over a mysterious planet in an unknown location.

Deploying ground forces to search for Anders, the UNSC and Covenant forces come under attack from a previously undiscovered alien organism - the Flood. Managing to regroup and hold a defensible location, the UNSC forces manage to locate the source of the signal - an apparent body of water. The UNSC forces withdraw back to the Spirit of Fire as a concentrated Flood force begins to gather momentum, narrowly escaping annihilation, regrouping at the Spirit of Fire over the lake - which splits to reveal an entrance, and with swarms of Sentinels emerging to deal with the Flood. The Spirit of Fire manages to enter, proceeding through a docking system, removing Flood growths and moving through a system of concentric rings that filters out Flood biomass, the Spirit of Fire emerges inside a massive Shield World, immediately engaging a Covenant Destroyer and fending off attacks while conducting repairs.

The Arbiter uses Anders to activate The Apex, revealing a fleet of Forerunner warships which the Covenant plans on reverse-engineering and incorporating into their existing naval forces to crush the humans quickly, without needing to dedicate all of their existing forces to the war. Anders manages to escape, using what had been her stasis prison as a translocation device, teleporting to the surface of the Shield World's interior, linking up with Forge and his Marines, who clear the area of Covenant forces and establish a base of operations on the Shield World. Removing the Spirit of Fires FTL Reactor, the UNSC move it into The Apex, planning to detonate it - the chain-reaction will send the Shield World's sun into a supernova, destroying the installation and the fleet, denying it to the Covenant and saving humanity from near total defeat and extinction. The Arbiter attempts to stop them, but his Honor Guards are killed by Red Team, and Forge himself manages to kill the Arbiter with one. Now unable to return to UNSC space with the speed an FTL drive would have afforded them, the Spirit of Fires crew enter cryonics storage. The ship begins its long journey home, likely to take many years or decades. Here, Sgt. Forge's cryo tube is closed by Captain Cutter, who briefly nods, upon which the camera pans down to find the words "Sgt. J. Forge," acknowledging the sacrifice of the valiant Marine Sergeant.

In the final moments of the credits, Serina speaks the final words of the game, saying "Captain. Wake up. Something has happened," As the logo appears on the screen.

The ultimate fate of the Spirit of Fire is unknown. Investigations by the UNSC and ONI are officially closed a few years after it is officially designated MIA, but there is some evidence that the ship does at some point return to UNSC space, with the strongest argument being the number of Spartans present during the Fall of Reach; At the time, 25 of the remaining 28 are present on the planet, with the three missing identified as Gray Team and the remaining dead or missing all previously identified, leading credence to the idea that Red Team, do eventually reunite with the UNSC. However it is noted that since Spirit of Fire's crew were the first humans to encounter the Flood, information should have been reported to ONI, but the first recorded Human-Flood encounter was in 2552, 21 years later, on Halo Installation 04, meaning that either the Spirit of Fire did not come back or ONI kept the 2531 Human-Flood encounter a closely guarded secret.