With the United Nations Intelligence Taskforce providing security, the British space programme under Professor Ralph Cornish oversees the launch of the Recovery Seven probe. This has been sent to Mars to make contact with the missing Mars Probe Seven and its two astronauts, who lost contact with Earth eight months earlier. The pilot of Recovery Seven, Van Lyden, makes contact with the Probe but is then silenced by a piercing unearthly sound. The noise troubles the Doctor who travels with his assistant Liz Shaw to the Space Centre to investigate the situation, offering insights into the origin and meaning of the sound, which he interprets as coded messages. He also identifies a reply message sent from Earth and this is pinpointed to be coming from a warehouse seven miles away. Led by Brigadier Lethbridge-Stewart, UNIT troops attack the warehouse and engage in a gun battle with troops organised by General Carrington.
Meanwhile Recovery Seven has returned to Earth and while UNIT is transporting it more of Carrington’s troops stage an ambush and steal the vessel. The Doctor relocates it, by which time it is empty. Carrington has ensured the contents – three space suited astronauts – are detained elsewhere, feeding them radiation to keep them alive. Carrington is now introduced to the Doctor by Sir James Quinlan, the Minister for Technology, who explains that he is head of the newly formed Space Security Department, and that his actions were to protect the astronauts as they had been infected with contagious radiation. Quinlan states that they did not want the public to become panic-stricken and so Carrington had been acting with authority in his actions.
By the time Carrington takes the Doctor and his friends to meet the astronauts the situation has changed again. A criminal named Reegan has organised their abduction, killing the soldiers and scientists protecting them. When the Doctor and Liz examine the situation they work out that human tissue could not have withstood the degree of radiation emitted to the astronauts, who are still in orbit, meaning the three space suits contain alien beings instead. Reegan now engineers the kidnapping of Liz Shaw to aid his own scientist, Lennox, a disgraced Cambridge professor, in maintaining the alien beings while they are incarcerated. Together they build a device to communicate with and control the aliens, who are sent on a killer rampage at the Space Centre, killing Quinlan and others. Liz later helps Lennox escape, but his bid for freedom is cut short by Reegan’s merciless revenge.
Despite the obstruction of the authorities, Ralph Cornish is determined to organise another space flight to Mars to investigate the situation. With Quinlan dead, the Doctor now decides to pilot the Recovery Seven probe ship himself. As he prepares to blast off Reegan tries to sabotage the probe by increasing the feed of M3 variant, but the Doctor survives the attempt on his life and succeeds in piloting the probe so that it connects with an enormous space craft orbiting Mars. Aboard the spaceship the Doctor discovers the three original astronauts are unharmed but mentally deluded into believing they are in quarantine. An alien being now reveals itself to the Doctor and explains the humans are being held aboard the craft pending the safe return of the Alien Ambassadors. They had been sent to Earth following a Treaty between the race and mankind, but the terms of this agreement have now been broken because of the detention of the Ambassadors. The Doctor offers his personal guarantee to help return the Ambassadors to their mother ship and resolve the conflict before a state of war is declared, and is permitted to leave the alien craft and return to Earth.
When the Doctor touches down he is gassed and kidnapped by Reegan, who takes him to Liz. Reegan’s real paymaster and the real organiser of the situation is revealed to them: General Carrington. The General reveals his actions have been prompted by xenophobia driven by his own encounter with the alien beings when he piloted Mars Probe Six some years earlier. His co-pilot, Jim Daniels, was killed on contact with the aliens and the General signed the treaty with the aliens to lure three of their number to Earth, where he hoped he could unveil their real agenda of alien invasion. The use of the ambassadors to kill people was similarly done to arouse public opinion against them. The next phase of his plan is to force the Ambassadors to confess their plot on public television. Leaving the Doctor and Liz working on a new and improved communication device to translate the aliens, Carrington departs for the Space Centre, where he aims to unmask the alien Ambassador before the eyes of the world – and then call on the powers of the Earth to blast the spaceship from the skies.
UNIT soldiers raid the secret base and rescue the Doctor and Liz, apprehending Reegan and his thugs. The Doctor races to the Space Centre and he and the Brigadier apprehend Carrington before he can make his broadcast. Sadly, he is taken away, protesting he was only following his moral duty. The Doctor arranges for Cornish and Liz to send the Ambassadors back to their own people, after which the three human astronauts will be returned.