In his introduction to the anniversary edition of Trollslayer, King explained that, after writing several short stories featuring Gotrek and Felix, he was commissioned to write a novel, and instead wrote two novella-length stories, which eventually formed the final chapter of Trollslayer and the first chapter of Skavenslayer.
Having arrived in the Imperial city of Nuln, Gotrek Gurnisson and Felix Jaeger have found employment as sewerjacks. While patrolling the sewers with their squad they surprise a human noble conducting a clandestine meeting with a skaven rat-man. The skaven kills their squad sergeant with poison gas but is itself killed by Gotrek's thrown hatchet. The sewerjacks flee the gas cloud and return to the surface.
That night Felix's brother Otto finds him at the seedy inn where he is staying and invites him to dinner. At the Golden Hammer restaurant Felix is shocked to recognize the man from the sewers, whom Otto informs him is Fritz von Halstadt, Chief of Countess Emmanuelle's secret police. Von Halstadt has secretly been using the skaven as spies in his efforts to root out mutants within the city, unaware that the rat-men are manipulating him into removing powerful figures so the city will be weakened for their planned invasion. Von Halstadt decides that the sewerjacks must die to protect his identity and works with the new skaven leader, Grey Seer Thanquol, to have them removed. Thanquol sends his rat-ogre bodyguard, Boneripper, to kill twin sewerjacks Hef and Spider. Galvanised by the murder of the twins, Gotrek, Felix and Rudi, the surviving members of the patrol, break into Von Halstadt's house via a secret entrance they discover in the sewers. Felix goes upstairs to Von Halstadt's study and confronts him, killing Von Halstadt in a duel despite the latter's superior skill. Thanquol and Boneripper arrive for a meeting with the corrupt man and Boneripper kills and eats Rudi who stayed behind to guard the exit. They hurry upstairs towards the sounds of fighting but are stopped by Gotrek, who cuts Boneripper in half and sends Thanquol fleeing. Gotrek and Felix torch the house before leaving via the sewers.
Kicked out of the sewer-watch after Gotrek assaulted the watch captain for refusing to believe their report on the skaven and bailed out of jail by Otto, Gotrek and Felix are employed by Gotrek's old mercenary friend Heinz as bouncers in his tavern the Blind Pig. Felix begins sleeping with tavern-girl Elissa after rescuing her from some thugs. Grey Seer Thanquol decides to have the pair eliminated and sends a team of skaven Gutter Runner assassins under Chang Squik to kill them. The first group try to ambush Gotrek but he turns the tables on them and kills them all before raising the alarm. The second group break into Felix's room while he is in bed with Elissa but they both escape and the pursuing assassins are attacked by the armed patrons of the Blind Pig, who slaughter them.
Heskit One-Eye, leader of the Clan Skryre element of the skaven army gathered in the tunnels beneath Nuln for the invasion of the city, plans a raid on the College of Engineering. Grey Seer Thanquol learns of the planned raid through his underling Lurk Snitchtongue, whom he uses to send a mysterious warning (in badly-spelled Reikspiel) to Gotrek and Felix, alerting them to Heskit's plans in the hopes that they will either foil the raid, preventing his rival from gaining prestige and potentially usurping him as leader of the skaven army, or die in the attempt, thus ridding him of two dangerous enemies. Breaking into the College of Engineering on a night when most of the engineers are at the palace for a banquet thrown by Countess Emmanuelle, Gotrek and Felix discover the skaven of Clan Skryre stealing human technology. Heskit One-Eye mans a Steam Tank to try and kill the interlopers but confuses his own followers into thinking he is attacking them. Fighting his way through the chaos, Felix ends up inside the steam-tank with Heskit as it barrels out of control, smashing through a wall before falling through the hole into the sewers the skaven used for their raid. Felix and Heskit both escape from the tank shortly before it explodes and both sides flee the scene.
Plague Monks of Pestilens
Vilebroth Null, leader of the Clan Pestilens element of the skaven army gathered beneath Nuln, begins with the help of his followers brewing a plague to kill the population of the city. Lurk Snitchtongue overhears him making plans and warns Thanquol, who once again uses Lurk to send a warning message to Gotrek and Felix. Worried that both he and Elissa have fallen ill Felix asks Otto to help them, and Otto sends them to Doctor Drexler, a highly educated and reassuring man who diagnoses them both with simple colds. Felix accompanies the doctor to the morgue in the Gardens of Morr in an attempt to discover the source of the plague and eventually deduces that the illness is spreading from the Gardens themselves. He and Gotrek break in under cover of darkness and discover Vilebroth Null and his plague monks brewing the plague in the Cauldron of a Thousand Poxes. The duo kill all the monks and Felix nearly drowns Null in his own cauldron before the skaven uses magic to teleport away and save himself. Gotrek destroys the cauldron before they leave.
Beasts of Moulder
With the plague spreading through Nuln and people dying in droves, Izak Grottle, leader of the Clan Moulder element of the skaven army, devises a plan to deprive the people of Nuln of their food. His followers breed a strain of rats with insatiable appetites and plan to release them into the city where they will devour all available foodstuffs. Lurk Snitchtongue learns through a drunken cousin who serves Clan Moulder of the plan and warns Thanquol, who once again sends him with a warning to Gotrek and Felix. Felix has been arguing with Elissa after the return of her jealous previous lover, Hans, and with the situation in the city worsening she and Hans leave together. Gotrek and Felix intercept the barge carrying Clan Moulder's rats and easily dispatch the skaven manning it, though one underling escapes with a single cage of rats which he accidentally releases in the sewers, meaning that soon both the city and the skaven tunnels will be infested.
The Battle of Nuln
The situation is grim both in Nuln and the skaven tunnels beneath it. The plague has mutated to affect skaven too and Thanquol's soldiers are dying like flies while above ground the humans die at the same rate. Clan Moulder's rats are breeding out of control and eating everything. Thanquol devises a plan to take the city before it is too late, on the night of a masked ball at the Elector-Countess's palace. He sends Chang Squik and his gutter-runners to infiltrate the palace and deploy a teleportation device he will use to appear inside the walls with his elite stormvermin soldiers and kill the Countess. Deciding to rid himself of Heskit One-Eye, Vilebroth Null and Izak Grottle once and for all he plans to deploy them near the Blind Pig and hope that Gotrek and Felix will kill them. Lurk's role as Thanquol's agent is compromised when Heskit, Null and Grottle capture him and decide to turn Thanquol's tactic against him, sending Lurk with a message to the pair warning them of Thanquol's attack on the palace hoping they will kill the Grey Seer. However, Felix spots and chases Lurk and his panicked flight is mistaken as a signal, causing the skaven units begin the attack too early. In the palace Chang Squik incorrectly deploys the teleportation device in a latrine, delaying Thanquol's attack when he and his stormvermin arrive, before fleeing the Grey Seer's wrath and accidentally mingling with the masked ball as the drunken revellers assume he is a human in a skaven costume. Battle breaks out in the streets and Gotrek, Felix, Heinz and the mercenaries from the Blind Pig fight for their lives against hordes of ratmen. Heskit One-Eye is killed when a burning building collapses on him and Gotrek cuts down Vilebroth Null, but Izak Grottle and Lurk both escape the battle. Finally looking at the warning message delivered to him Felix learns of the threat to the Countess and rallies the people of Nuln to march to the palace.
In the ballroom Thanquol arrives and begins randomly murdering nobles with sorcery, demanding that Emmanuelle step forward but unable to make himself understood. He takes the opportunity to kill Chang Squik for his failure as well. Eventually Emmanuelle comes forward but at that moment Felix and Gotrek burst in. Thanquol tries to blast them with warp-magic but Doctor Drexler who is in attendance shields them with his own magic. The tables turned, Thanquol flees through the closing portal in the latrine.
The people of Nuln begin rebuilding their city. The plague abates and all the rats die. A messenger arrives at the Blind Pig with a missive for Gotrek, who upon reading it tells Felix to pack his bags. When Felix asks for details, Gotrek says only that a mighty doom awaits.