Within the first few pages of the book, the Yellow launch a worldwide aggression with modern rockets, bombers and paratroopers that quickly destroy and conquer the world's other major powers.

Forewarned of the attack by a traitor in the Yellow army, Captain Francis Blake, a British officer, and Professor Phillip Mortimer, the scientist developing the Swordfish, escape with the superweapon's plans, their destination being a secret base in the Middle East where they will be able to finish their work.

The rest of the episode follows their attempts to escape the pursuing Yellow forces, led by the cunning and conniving Colonel Olrik, Basam Damdu's chief of security.

They initially escape from Britain in a jet-powered airplane called the "Golden Rocket", but are shot down somewhere over Iran by Yellow interceptors, and must continue the trek to the secret base on foot.

The episode ends with a cliffhanger: the soldiers of the Yellow army are directed to the room where Blake and Mortimer are staying and as they enter they find an astonishing surprise (naturally the reader can only see their reaction, not the cause of it).

This sparks an immediate insurrection in which the outraged townsmen quickly massacre the Yellow troops; in the ensuing chaos, Blake and Mortimer emerge from hiding and take off again, still with Nasir helping them.

As chief of the Empire's security service, Olrik is the natural scapegoat for this state of affairs; he therefore decides to take the gloves completely off and torture Mortimer as harshly as necessary, hoping to finally elicit a confession.

After this, in the secret base, Blake and the admiral in command, Sir William Grey, have been conducting resistance against the Yellow (including many of the incidents that Olrik is being blamed for).

Olrik then deploys new chemical weapons against the base, which allow the Yellow to gain a foothold and slowly begin to work their way inwards, but both Mortimer and Grey keep their word, and the two Swordfish (designated SX1 and SX2, hence the title) are finished in time.

In the following week, open rebellions erupt worldwide, taxing the overextended resources of the Yellow to the limit until the Emperor decides to end the war by launching ICBMs against all the rebel targets (with Olrik strapped to one of the rockets as punishment for his failures).

Before he can do this, however, an entire squadron of Swordfish arrives over Lhassa and nukes the city, killing Basam Damdu and decapitating the Yellow Empire under Olrik's mocking eyes.