Published in 1993 and set after the events of Wing Commander II: Vengeance of the Kilrathi, the majority of End Run centers on a minor pilot from that game, Jason "Bear" Bondarevsky, recently assigned to the escort carrier TCS Tarawa as her flight group's Wing Commander.
The first part of the novel, written by Stasheff, centers on the TCS Johnny Greene, a Venture-class corvette assigned to picket duty on the front lines, a guard against Kilrathi raiders. Aside from stops at base to pick up more perishables, the Greene has been on station for two years, and has picked up a number of unconventional modifications, such as two extra engines salvaged from a Kilrathi ship. In the opening scene, the ship's oxygen regeneration plant is damaged, and Captain Macmillan Harcourt orders a return-to-base.
Unexpectedly, the Greene is diverted, from the provocatively-named Xanadu Base to an unknown backwater called Hilo. Here, Harcourt and his crew are recruited for a reconnaissance mission on a Kilrathi dustball called "Vukar Tag." So far as anyone can tell (explains the recruiter, Captain Tor Ripley), there's nothing special about Vukar Tag: no ore deposits, no natural resources, no nothing. So why is there a cruiser and several wings of fighters in the system? Harcourt happens to be curious enough to find out.
There will also be a mission specialist, Lieutenant Commander Ramona Chekhova, who will be in charge of the cameras and surveillance equipment. Aboard his own ship, the captain (Harcourt) is the only reigning monarch, but because of disparities in Navy and Space Force pay grades, Ramona technically outranks him, and attempts to exert her influence over him and the Greene's crew as soon as possible—which leads only to her public humiliation.
At Vukar Tag, though, there is no time for petty power struggles. Hiding in a local asteroid belt, the crew attempts desperately to figure out how to elude the system's defenses, make a single orbit of the planet, and get out again. The main problem is that if anything approaches the planet, the Kilrathi are apt to shoot it down first and ask questions later... A fact proven by the discovery of a wrecked Venture-class corvette in the asteroid belt. The Greene is the third reconnaissance mission sent to the Vukar Tag system, a fact Ramona knows but Harcourt did not.
But it's the wreck of that corvette, the John Bunyan, that saves their mission. Ramona will use it for her fly-by, while the Greene attacks a passing supply convoy as a distraction. Hopefully, the Kilrathi won't notice Ramona until her slingshot orbit sends her back to the asteroid belt, but she'll send them the pictures by radio if she has to—the most important thing is that the Greene return to Confed space with the data. If necessary, she orders Harcourt, the Johnny Greene will leave her behind.
Which is, in the end, what happens. The Greene proves a marvelously successful distraction, but at least one Kilrathi is clear-headed enough to notice the John Bunyan, and Ramona is taken out. But not before she manages to send all the data she's collected up until then... And not before she finds what is undoubtedly the reason for all the security around Vukar Tag: a beautiful fairy-tale castle, all alabaster spires and minarets. This data safely in hand, the Johnny Greene returns to Confederation space... And the waiting war.
Jason's pilots are green and raw, but the Tarawa is expected to remain away from the front lines; it's hooking up with the First Marine Commando Battalion and escorting them to a new sector. Jason takes this time to teach his pups everything he can about fighting the Kilrathi and staying alive while doing it. The most promising pilot in his wing is Kevin "Lone Wolf" Tolwyn, nephew to Admiral Geoffrey Tolwyn. Kevin has killer instincts and a definite aptitude for the job, but a pampered upbringing has left him spoiled and conceited. The job is further complicated by the fact that this Marine battalion in question, the "Cat Killers," is the home of Jason's old flame, Svetlana Ivanova, who flew under the call sign "Ice Princess" before flunking out of flight school. An acrimonious break-up led to her joining the Marines, and at first meeting, it appears nothing has changed—she still hates him.
The First Battalion brings news as well: Tarawa's destination has changed. It and the Marines will be joining fellow escort carrier TCS Sevastapol for a strike at a worthless ball of dust: Vukar Tag. The Marines, under command of Brigadier General "Big" Duke Grecko, have orders to seize the fairytale castle, loot it and destroy it; Tarawa's wing will provide cover and atmospheric interdiction, while the Sevastapol's flight group keeps space pacified. The mission is a success, and in the end, Jason is impressed with the performance of his pilots; a few planes are damaged, but the only loss is from a damaged and retreating Sabre... Which Jason assigned Kevin Tolwyn to escort back to the Tarawa. A lone Sartha light fighter sortied up, and Jason ordered Lone Wolf to stay with the Sabre; but Tolwyn, claiming radio damage, gave chase. The Kilrathi had heavier fighters lying in wait; one of the Sabre's crewmembers is lost when he fails to eject in time. Jason busts Tolwyn for disobeying orders and removes him from the flight roster until further notice, but comments to Doomsday that they will need his killer instinct if they intend to win the war.
The one oddity about the strike, which is almost textbook, is that Grecko forces Jason not to destroy a Kilrathi transmitting post, which undoubtedly manages to get off transmission to Kilrathi territory. The confusion increases when the Tarawa and the Marines are pulled off Vukar Tag within twenty hours and sent to a rendezvous point. There they find most of the Third Fleet: the Concordia, the Bengal-class Wolfhound, the Trafalgar and Jason's former home, the Gettysburg. Admiral Banbridge, commander Third Fleet, explains the plan: the castle on Vukar Tag was the ancestral home of the Kilrathi Emperor's Dowager Mother, and the transmitting post was left intact so that news of its destruction might be relayed as quickly as possible. This attack will be received as a grave insult, and Kilrathi honor will leave the Emperor and Crown Prince Thrakhath no choice but a crushing retaliation—especially when Terran Marines start fortifying, as if they plan to turn Vukar into a permanent base. When the Imperial Home Fleet, ten carriers in total, is fully engaged in the ground assault, the Third Fleet will jump in, ambush them and destroy them. Jason is not the only one to notice, however, that the Third Fleet is only four carriers strong, and consists of half of the Confederation's remaining strength. If Vukar backfires and the Confederation contingent is destroyed, the Kilrathi will win the war.
Jason, Svetlana, her commanding officer Col. Merritt, and Captain O'Brien are drawn aside after the briefing; inside the room is Admiral Banbridge, Admiral Tolwyn, Captain Teng of the corvette Kagimasha and Captain Grierson of the destroyer Intrepid. When asked by Banbridge, Jason expresses his doubts about the plan; this segues directly into why Banbridge has pulled them aside. Tarawa, Intrepid and Kagimasha are named "Strike Force Valkyrie," with but one goal: to attack the Kilrathi homeworld of Kilrah. They are to slip in using jump points the Kilrathi thought were secret, and make their way directly to the Kilrah system, where they should attack to the best of their abilities. On their way, however, they must allow themselves to be seen. Hopefully, this will convince Thrakhath to split his fleet, sending a few carriers home while leading the rest on to Vukar. Against six or seven carriers, the Third Fleet has a much better chance. Unfortunately, Strike Force Valkyrie has no such chances. The Tarawa is expendable. Officially, Banbridge declares, they're on their own; but after the briefing, Tolwyn makes Jason an unofficial promise: if he can, he'll take the Concordia in from Vukar and cut them out. If Jason and his crew are to be expected to sacrifice everything to save their compatriots at Vukar, then Tolwyn expects no less of himself and his own.
The mission launches. Though Jason and Svetlana manage to rekindle their romance, Captain O'Brien's cowardice proves a constant ordeal, and Jason frequently has to strong-arm him into sticking with the plan. Jason has been assured by Admiral Tolwyn that if he needs to lead a mutiny—for the second time in as many years—he will have Tolwyn's support, but Jason isn't sure that'll be enough. Fortunately, he doesn't have to make the choice. Tarawa and her escorts arrives in the Kilrah system ahead of the returning enemy carriers, and move to strike Kilrah's second moon, a giant carrier construction facility housing six uncompleted ships (it is later revealed that this moon constitutes a third of the Kilrathi's total shipyards). While the Marines are on the surface, setting up demolition charges and killing the shipyard workers (who will take years to replace), the Kilrathi carriers arrive, and Tarawa comes under direct attack; a kamikaze hit takes out the bridge and everyone on it, and Jason, as the ranking officer, assumes command.
Tarawa hangs at the second moon for as long as possible, giving the Marines time to finish their job, and then calls for an immediate recall. Most of the Marines make it up. Svetlana Ivanova, unfortunately, is not one of them. Grief-stricken and with Kilrathi reinforcements practically on top of them, Jason takes his fleet deep into one of the system's gas giants (Igratha) to repair and plan their next move. Prince Thrakhath, in personal command of the home system hunt, is left to ponder what will happen next.
Jason's next move is daring: Tarawa, Intrepid and Kagimasha accelerate to ramming speed and plot a course directly towards Kilrah. As distractions, they drop several unpiloted ships with nuclear weapons aboard. In the meanwhile, they use their tractor beams and Kilrah's gravitational pull to slingshot themselves towards a jump point out of the Kilrathi system. The Kagimasha is rammed at over ten thousand kilometers a second and destroyed, but the other two ships survive the maneuver. The only problem, Thrakhath muses as he surveys the aftermath of the confrontation, is that the jump point they have chosen is a fairly slow line; Thrakhath can cover the same distance faster, using alternate points, and then cut them off. Destroying them will not be fit revenge for the disaster at Vukar, where the human ambush went off without a hitch, but at least it's something. Jason knows where his fleet is heading, but any exit is better than none. They'll aim for the Jugara system, where jump points lead back to human-controlled space. Maybe they can make it out.
The final battle takes place in the Jugara system. Thrakhath has maneuvered his three carriers to cover the main jump points out of the system, Tarawa and Intrepid both are wounded, most of Tarawa's external sensors have been destroyed, and the Terrans have only 20 fighters at their disposal. Even worse, scans detect a fourth carrier emerging from the jump point to Confederation space. Doomsday, with a re-instated Kevin Tolwyn on his wing, leads a strike against one of the carriers, but fails to destroy it. Kevin, unexpectedly, risks his life to keep Doomsday's crippled ship in one piece; he has found what he truly wants in life, and it has nothing to do with being a spoiled brat, but rather with having the heart-to-heart, life-and-death trust of his fellow pilots. That day, he earns it. But the Tarawa has taken critical damage, the Intrepid is lost, and, finally, Jason orders the crew to escape pods so that he can ram the nearest Kilrathi carrier. Doomsday and Kevin arrive just in the nick of time: Tarawa, with its radio destroyed, did not hear Admiral Tolwyn's message when his Concordia, the fourth carrier, emerged from the jump point. The Tarawa is saved. Everyone is going home.
The final chapter wraps up at the rendezvous point. The Gettysburg will need to be drydocked and the Trafalgar is destroyed, but five of the seven Kilrathi carriers at Vukar were smashed, and thousands of their finest marines as well. Banbridge is furious at Tolwyn for disobeying direct orders to remain at Vukar after the battle, but because they're all heroes now, he can hardly complain. The Tarawa and its crew are galaxy-wide celebrities, and with good reason: it took four human carriers to destroy five Kilrathi ones in space, but Tarawa killed six on the ground, and then fought her way out against overwhelming odds. The Tarawa herself is practically a wreck, but though it should be scrapped (and it'd be cheaper to just build a new one), she will be repaired and rejoin the fleet, the First To Kilrah, with Captain Jason Bondarevsky at her helm. Doomsday replaces Jason as Wing Commander. And as for Kevin, Admiral Tolwyn couldn't be prouder: the boy has come back a man. Tolwyn joins the Tarawa crew in Jason's previous spot as Rapier squadron commander.