Alistair Gordon Lethbridge-Stewart has long since retired, both from soldiering and from teaching, and assures his wife Doris that his "blood and thunder days" are long past. But a sword is calling for help, and a UNIT convoy has been stranded near Vortigern's Lake by an unexpectedly fierce thunderstorm. The TARDIS materializes in response to the sword's call, which is crossing even the boundaries which separate alternate timelines. The Doctor and Ace hitch a lift to the lake with Professor Peter Warmsly, who is shocked to find a UNIT convoy parked on top of his archaeological dig. The Doctor is more concerned with the convoy's cargo, which is nuclear, and with the strange sounds he and Ace can hear -- sounds like missiles being fired. In fact, the "missiles" are armoured knights who have travelled from an alternate timeline...

The Doctor seeks answers from the soldiers at the convoy but is unceremoniously turfed out by the new no-nonsense Brigadier Winifred Bambera. Bambera drives the Doctor and Ace to the nearby Gore Crow Inn, where Warmsly is trying to contact someone in authority to get the convoy off his land. The Doctor notices a scabbard on the inn's wall, which Warmsly identifies as one of his finds from the battlefield dig. "The scabbard's worth ten of the sword," but where's the sword?

Bambera contacts UNIT control to inquire about the stranger who calls himself the Doctor, and word gets to Lethbridge-Stewart, who comes out of retirement to help deal with the possible emergency. He appears to be doing so reluctantly, but Doris isn't fooled--or pleased that he's risking his life.

The leader of the Grey Knights, Mordred, also recognizes the Doctor as Merlin, and the Doctor successfully frightens Mordred into leaving -- but admits to Ace that he hasn't the faintest idea who any of these people are. He and his friends retreat to the inn, while Bambera's attempt to interrogate Ancelyn quickly degenerates into hand-to-hand combat -- which Bambera wins, to Ancelyn's surprise. Night falls surprisingly quickly, and when the scabbard comes to life and flings itself across the room, the Doctor realizes that the timelines are being fractured. Mordred, realizing that he's outclassed in the fight, has opened a gateway in a ruined church nearby, and is calling on his mother, the sorceress Morgaine. Morgaine steps into the new world from her own and telepathically contacts the Doctor, ordering him to give up the fight. The Doctor, however, refuses to stand by while one timeline's battle is fought in another world. So he and Morgaine will fight once more.

The next morning, the Doctor and Ace accompany Warmsly to the dig, where he shows them a cryptic message carved on an ancient rock. The Doctor translates the inscription as "Dig Hole Here", written in his own handwriting. Ace blasts a hole in the middle of the dig, revealing the opening of a tunnel which appears to lead under the lake. Warmsly sits back in shock, staring at the ruins of his dig while the Doctor and Ace enter the tunnel.

Lethbridge-Stewart approaches the town, piloted by young Captain Laval in a helicopter. Morgaine witnesses the helicopter's approach, and casually uses her mental powers to shoot it down. Laval is injured in the crash, and Lethbridge-Stewart sets off to find help. Morgaine, meanwhile, realizes that she fired from the grounds of a cenotaph, and has lost honour by desecrating a memorial of the war dead. She blames Mordred for misleading her about the natives' primitive customs, and as Mordred, sulking, storms off, Morgaine has her troops hold an impromptu ceremony to ask forgiveness of the dead. Lethbridge-Stewart happens across her during the ceremony, and helps her to conduct it properly, in return for which she allows him free passage into the town. Lethbridge-Stewart meets Shou Yuing and commandeers her car to get to the dig.

The Doctor recovers and manages to expel Ace and Excalibur from the ship, but he is then attacked by the snake and nearly killed. Lethbridge-Stewart arrives, just in time to rescue him. Ace rises from the lake holding Excalibur, much to Warmsly's shock.

Mordred is making a nuisance of himself at the Gore Crow Inn, terrifying innkeeper Pat Rowlinson and his blind wife Elizabeth, when Laval arrives, looking for a phone. Morgaine arrives to collect her son and takes the opportunity to drain Laval's knowledge of UNIT troop strengths out of her mind, casually blasting Laval's body to ash when she's finished. She then saves honour for Mordred's actions by restoring Elizabeth's sight.

Morgaine orders her troops to block the road from the convoy to the inn, but the Doctor, the Brigadier, Warmsly, Ace and Shou Yuing run the barricade and get through with Excalibur. Bambera and Ancelyn, following behind, are run off the road and the others look back to hear an explosion and see a cloud of smoke. Subdued, they continue on to the inn, where UNIT troops are evacuating the civilians. The Doctor hypnotises Pat Rowlinson and Warmsly, convincing them to leave quietly without kicking up a fuss, but Ace helps Shou Yuing to hide behind so she won't miss the excitement. The Brigadier proudly points out the weapons his troops have brought, and the Doctor, perhaps jokingly, asks if he has any silver bullets.

UNIT soldiers find the remains of Bambera's car, but no sign of her or the knight. The Brigadier realizes that if she's survived, Bambera will be trying to return to her convoy -- and will be leading Morgaine's troops into a pitched battle with UNIT forces with an armed nuclear missile on the battlefield. The Brigadier reveals that he's had the Doctor's old car Bessie brought to the fray, and before leaving, the Doctor gives Excalibur to Ace and Shou Yuing, telling them to draw a chalk circle on the ground and stay inside with the sword.

The Doctor threatens to kill Mordred unless Morgaine leaves his friends alone, but Morgaine knows he's bluffing. The Brigadier, however, has a gun, and he isn't bluffing. Mordred is horrified when Morgaine sadly bids him goodbye and orders her knights to kill everybody at the battlefield in revenge for her son's death. She then orders Ace and Shou Yuing to hand over Excalibur, or she will release the Destroyer from her control--and once free, he will devour the world. Meanwhile, realizing that killing Mordred would do no good, the Brigadier takes him prisoner and they return to the inn with the Doctor. The battle continues behind them, and eventually, the UNIT forces emerge victorious on a field littered with bodies.

They arrive just as a gigantic explosion tears the inn apart, and in the confusion Mordred escapes. The Doctor enters the remain of the inn, only to find Ace and Shou Yuing still alive; rather than risk the wrath of the Destroyer they handed over Excalibur. Ace is surprised and pleased when the Doctor admits this was just as well. The vortex tunnel to Morgaine's hideout is still open, and the Doctor and the Brigadier leap through to confront the witch and her demon. Ace pauses only to collect a box of silver bullets and follows them.

As the Doctor and the Brigadier confront Morgaine, Ace arrives just in time to distract Morgaine and gives the Doctor the opportunity he needs to reclaim Excalibur. Morgaine threatens to release the Destroyer, who admits that he deliberately left the tunnel open so the Doctor could follow them and seize Excalibur, so that Morgaine would be forced to release him and he could devour the world. The Doctor feels sure that Morgaine is just bluffing and is quite surprised when she releases the Destroyer, who breaks his bonds and begins swelling with power. She seizes the sword and prepares to return to her home dimension, but at that moment Mordred arrives and accuses her of betraying him. While Morgaine is distracted by the sight of her son turning up alive after all, the Doctor grabs Excalibur once again just as she and Mordred pass through the gateway and vanish.

There's still the Destroyer to deal with, and the Doctor makes sure Ace and the Brigadier are safely out of harm's way and then tells Ace to hand over the box of silver bullets. The Brigadier, however, knocks the Doctor out and then returns to the ruins to shoot the Destroyer himself. He is nearly killed in the resulting explosion but survives, and vows that this will be his last fight. The Doctor decides to awaken King Arthur and let him finish the fight.

The Doctor, Ace, Ancelyn and the Brigadier return to Arthur's spaceship, where Ace slots Excalibur back into place, bringing the ship back to life. Arthur, however, simply crumbles into dust, and Ace finds a note written by the future Doctor which reveals that the story of Arthur's survival and return was just propaganda--and that Morgaine has returned and seized control of the nuclear missile.

Morgaine drains Bambera's mind of the launch codes, and orders Mordred to dispose of her. Ancelyn comes to her rescue, and while he and Mordred fight, the Doctor confronts Morgaine, who is willing to destroy the entire area, herself included, to prevent Arthur from awakening and leading a war to depose her rule. The Doctor manages to convince her that provoking an accidental nuclear war would be a grossly dishonourable act, and at the last moment she agrees to let him shut down the missile. He then reveals that Arthur is dead, and this news crushes her spirit; Arthur had been her lover before they found themselves fighting on opposite sides. The Doctor leaves and knocks out Mordred just as he's about to kill Ancelyn, and advises the recovering Bambera to lock up both Morgaine and her son.