The novel opens on July 25, 2004 - Judgment Day. USMC Sergeant Justo Orozco and his men of the USMC Eleventh Marine Expeditionary Unit are running a drug-interdiction exercise with the Mexican Army in Baja California. It is here they witness the rise of Skynet - they suddenly see the opening shots of the War Against The Machines when Skynet's nuclear missiles hit the nearby cities of San Diego, Twentynine Palms and Hermosillo. Upon seeing the end of their old lives, the men, shell-shocked and frozen with fear, ask Orozco for new orders. Orozco takes the lead and assures them "We'll be all right. We'll survive, because we're Marines, and that's what Marines do."
The story jumps forward to post-Judgment Day in Los Angeles, where John Connor, serving as commander and leader of an independent organized Resistance cell group stationed in the area (as, though destined to lead humanity to ultimate victory, is still just a common soldier). The cell, while effective in operations against Skynet's local presence, is continuously and dangerously short on dwindling precious supplies and weapons, and Command regularly writes them off as they don't see any reason to take on their group on a permanent basis. Despite this, all of the men and women under his command have much respect for him, and are willing to sacrifice themselves on John's orders, especially Barnes, John's right-hand-man, and Blair Williams, one of the cell's few pilots.
After returning from an operation - coordinating with other cells to destroy most of Skynet's local radar towers, the makeshift base John's cell is occupying is attacked by Skynet forces as it's occupants sleep, but it is prevented when John gains advance warning after finding the base's lookout dead, having been taken out by a long-range sniper, and Barnes spots 8 T-600's moving in on the base. Barnes delays Skynet's assault by destroying a support beam of a nearby building, which collapses on the approaching Terminators. Not long after, the Resistance soldiers, ready for battle, evacuate the base, which is now under attack by multiple T-600's, T-1 tanks, and HK-Aerial's. Blair and Yoshi, the cell's two pilots, are ordered by John to get to their planes and get out as the rest of the personnel escape through an underground tunnel. As the cell escapes, Blair and Yoshi engage and destroy several of the HK's, but Yoshi runs out of ammo and has to rendezvous with the others at the fallback base. Blair destroys the remaining HK's and heads towards the base as well - but as she does so witnesses what appears to be an undiscovered Skynet Neighborhood-Sweep Staging Area; where Skynet establishes a carefully & expertly-concealed staging area with a force of Terminators and H-K's, calls in another force of Terminators to cordon off and seal the local area to prevent anyone leaving, and then sends out its troops to wipe out the local human presence again and again until all humans in the area are neutralized.
Upon rendezvousing at their fallback base, John contacts an unnamed General at Command, who, while sympathetic and thankful they escaped with minimal casualties, are once again opting not to aid them, even a partial re-supply, requested by John, is considered too great a risk at this time. Command then wishes them luck and disconnects to take another call.
In response to Command's constant abandonment of their group, John re-invigorizes his demoralized troops by declaring they will carry out a mission so spectacular and ground-breaking, everyone (i.e. Command, the other local Resistance groups and Skynet itself) will take notice, and convince Command never to write-off John's cell again. After receiving Blair's report on what she saw while in the air, it is concluded the Skynet base was a Neighborhood-Sweep Staging Area. The other senior members of the cell opt to destroy the Staging Area to get Command's attention, but to do so with their such limited resources sounds outrageous to the group. John's decision, however, sounds even more outrageous - capture the Staging Area intact, and John is able to convince the group it's the right course of action as it will convince Command of their usefulness. The group agrees to plan their assault to capture the Staging Area intact. Meanwhile, Kate Connor begins asking John to be allowed on field missions, insisting she could be of more use to them, and by extension solidifying her position as a leader. John, however, states she has more use in a support role (but in reality, it's because he feels he cannot risk her life).
John's cell quickly organizes their assault - when Skynet sends its Terminators out for the culling operation, the group's force of soldiers will be divided into two groups; one will make its stand in the neighborhood to keep the Terminators pinned down and destroy them before they can attack the local civilian survivor settlements, while the other will attack the Staging Area itself while it is relatively undefended. Both groups will have continuous air support from Blair and Yoshi. A side-objective of the mission is, while the force for the mission moves into the area to set up a staging area for the mission, it can also recruit new members for the Resistance from the local settlements.
Preparations for the assault begins, and Kate and Barnes lead a force to the local settlements to get recruits. The most significant of which is "Moldering Lost Ashes", where several hundred survivors are sheltering, living and working - the head of security of which is Orozco (who is implied to be the only remaining survivor from the Eleventh Marine Expeditionary Unit). Life at Ashes is difficult for Orozco for many reasons; he is the only professional military soldier present - and so really the only one recognizing the dangers surrounding them, and he is treated with a lack of respect from most of the population. The leader of the group; Chief Grimaldi, is a pompous, arrogant and unreasonable man who, having previously been a CEO of a corporation that made him rich and powerful before Judgment Day, is obsessed with his belief that Ashes (or as he insists on calling by its former name - Moldavia Los Angeles) is destined to be a thriving community once again - and performs actions that have left Ashes seriously endangered from the imminent Skynet assault, and deludes himself with denial about the deadliness of Skynet and it's forces, at least believing that keeping a low profile and staying out of Skynet's way is the only means of survival, at most Grimaldi harbors the completely suicidal belief that if the Terminators are left alone, they leave humans alone (which of course is completely idiotic). Orozco's only true friend is 16-year old Kyle Reese and his companion; Star, who Kyle looks after (and communicate in a form of sign language as Star doesn't speak). Kyle greatly respects Orozco, having gained his combat experience as a result of lessons given to him by Orozco. Orozco, in turn, looks after Kyle and Star as if they were his children, admitting that they are his two best friends in what's left of the world.
The Resistance group, when it visits Ashes, is greatly semi-warmly by Orozco, who immediately shares a silent bond with Barnes, but completely hostile from Grimaldi who, when the time comes and those among Ashes step forward to join the Resistance, Grimaldi, obsessed with keeping what he feels are his property, immediately draws his weapon on the Resistance group, and a stand-off ensues between them until Kate and Orozco break it up. When the handful of recruits leave with the Resistance group, Orozco, having realized by this point that the Resistance is planning something big in the area (explaining their presence), it must mean Skynet is finally making a move against Ashes and the other civilian groups, and so opts to stay to defend those he's sworn to protect. Nevertheless, having forgotten to inform Kyle and Star of the Resistance group's visit, Orozco sends the two off with a group of traders, in exchange for surrendering the entirely of the settlement's gasoline fuel supply.
Skynet steps up its plan of attack, and so forces the Resistance to mobilize sooner than expected. Skynet's forces are dispatched to attack the neighborhood. When the Terminators arrive at the Ashes, Grimaldi, having previously denied the idea of an attack, completely falls apart when he realizes Orozco and the Resistance itself was right all along. Orozco makes peace with his former-nemesis, and so Grimaldi effectively gives up leadership of the Ashes to Orozco; who proceeds to mobilize the Ashes' defenders for battle. The initial assault, which is met by a coordinated effort from the Ashes defenders and the cell's first group of soldiers, personally led by John himself, is beaten back, and Blair and Yoshi hold their own against the H-K's. However, Skynet sends out its reserve of Terminators and closes in its cordon, as well as dispatching it's force of Terminators to attack Ashes via. the back at the same time. Soon, absolute carnage reigns, where several Resistance soldiers and many Ashes defenders are killed, and Yoshi, his fighter crippled, deliberately crashes his plan into an H-K, destroying them both. Blair, meanwhile, is left with almost no ammo, with one H-K still active. Blair can still provide ground support for the operation, but to do so would mean sacrificing their ability to help Ashes. John reluctantly orders her to help the group and, sure enough, shortly after the Terminators overrun and massacre all inside the Ashes, including Grimaldi, and the Ashes building itself is destroyed by Orozco's pre-placed explosives.
Meanwhile, Kyle and Star, having been hunted by the Terminators at the cordon when the trader group was ambushed and wiped out, successfully destroy the Terminator hunting them and proceed to escape the area, John unknowing who Kyle was.
Meanwhile, Barnes' group, secretly joined by Kate, who's unusual behaviour has driven her to participate in the mission against her husband's specific instructions to the contrary, finally raids the Staging Area, and meet minimal Skynet forces inside. However, Blair finds another force of Terminators about the attack the compromised Staging Area. Just when it seems the operation will fail, the Resistance arrives in force - Squadron Five, the helicopter squadron under the personal command of General Olsen, arrives to support and reinforce John's cell, Command having been impressed enough by their efforts to have Olsen join the fray. Soon the tide is turned and Skynet's presence in the area wiped out. The Resistance, and more specifically John Connor, has triumphed.
After the battle, in the captured Staging Area, Olsen reports John's plan to get Command to take on their group permanently succeeded - they are being given a full slot in the Resistance structure, complete with all the benefits, and for starters is a brand new base, safe and secure, and away from the local wasteland of Los Angeles. Olsen reveals John's victory is bigger than even he imagined - the Staging Area was also a Skynet Maintenance Center (thus explaining why Skynet was so determined to defend the facility); with a great deal planned by Skynet for the local presence, until John and his cell captured the center and ruined it's plans. A massive amount of experimental and prototype Skynet weapons and other technologies are confiscated from the center for reverse-engineering and investigation for use against Skynet.
Meanwhile, a badly injured Orozco is retrieved out from the ruins of the Ashes, and treated by Kate, but Orozco surprises her by refusing to join the Resistance. Orozco, surrounded by the death and destruction around him, has grown tired of authority and the need to protect others, and feels that the generals and admirals leading the Resistance are basically the same as those who caused Judgment Day, and so he vows never to serve them again. Orozco, at his own request, is left behind. However, when he seems poised to spend the rest of his life in self-imposed exile, Orozco stumbles upon a group of 8 children, all survivors from the Ashes, having been hidden away by the local pastor, who felt they were worth saving for life after the massacre. Regaining his sense of duty, Orozco takes chargeof the children and leads them off to survive in the ruins, because "He was a Marine, and that's what Marines do".
The story ends as John's cell settles into its new base, when Kate, having finally realized what is really causing her unusual behavior, reveals to John she is pregnant - leaving him, for the first time in a long time, speechless.
- Terminator Salvation (novel) (official movie novelization - April 28, 2009)