October 1957. The Doctor, Ace and Benny visit New Mexico to observe the launch of an Atlas missile from the White Sands proving grounds, one of the first steps on mankind’s journey to the stars. Instead, they see two flying saucers shoot the missile down. Concerned, the Doctor takes Ace and Benny into town to speak with the locals, and learns that a number of flying saucers have recently been spotted in the area. The locals’ opinions differ as to whether they are military test flights, Soviet spy planes, or aliens from another world. Meanwhile, the discs buzz White Sands again, to provoke a military response so the aliens can analyse the humans’ ability to navigate and fight in three-dimensional airspace. Colonel Jack Finney orders an experimental new radar array into operation so his fighters can track the saucers through the darkness, and by the time Major Kreer from AFOSI learns what Finney has done it’s too late for him to intervene. The pulses from the array interfere with the discs’ gravimetric drives, and one of the saucers crashes into the desert, killing all aboard. Kreer orders Finney to send all of the wreckage to Corman AFB for the Moondust project -- and then secretly sabotages the array. However, he leaves a trip circuit in the array so he will be able to reactivate it should the need arise.

The next day, while taking Benny to a pueblo she feels may be of archaeological interest, the Doctor spots a number of unconscious bodies at a nearby farm. He and his companions determine that the family was captured by aliens, who took genetic samples from them and then erased their memories. The Doctor spots a smoke column rising nearby, and he and his companions discover the wreckage of the UFO. Before they can investigate further they are arrested and taken to White Sands for questioning, but the Doctor gets to a phone and contacts the head of the CIA. Allen Dulles owes the Doctor a favour, and he therefore orders Finney to give the Doctor all the help he needs to investigate matters here. As Finney fills in the Doctor, Ace notices a group of suspiciously blond, purple-eyed soldiers stealing two nuclear warheads from the base. She gives chase, but is unable to stop them. It appears that the Earth is being invaded, but why would the aliens wish to steal human nuclear weapons when they no doubt have superior technology of their own?

Captain Stoker takes the stolen warheads to Corman AFB, where he and Major Kreer are working on the top-secret Snowbird project under the paranoid, authoritative General Nyby. Nyby’s greatest fear is that the Communists are conspiring to overthrow his country, and he will do whatever it takes to ensure American supremacy. Stoker, meanwhile, finds himself experiencing inappropriate and irrational emotional surges, which appear to be explained when Kreer -- who wishes to spread dissension amongst his allies -- gives Stoker a photograph which proves that he was on Earth over six months ago. This comes as something of a surprise to Stoker, who was under the impression that he’d only arrived on the planet recently; however, when he thinks about it, he realises that his earliest memories are nothing but a blur. Meanwhile, Kreer himself struggles to resist the continuing genetic changes in his own body, and waits for his allies to give him the cure they had promised.

The Doctor, Ace and Benny return to the crash site, where they meet White Sands’ PR officer, Major Marion Davison. The Doctor identifies the UFO as a Tzun skiff, belonging to a highly skilled warrior race which will be wiped out by the Veltrochni in the year 2170 when a contact team accidentally incinerates the Veltrochni’s traditional incubation grounds. According to official history, the Tzun never made it out this far; something must have called them away from their home sector, in order for them to have come to Earth. Ace sees Stoker arranging the removal of the disc from the crash site, and recognises him as the man who led the raid on White Sands -- and the Doctor sees that Stoker is supervising the separation of the disc into sections, which should be beyond the grasp of contemporary human science. The Doctor also wonders why Stoker’s superior, Major Kreer, is not present at the recovery of a genuine alien artefact, and decides to investigate further.

Davison smuggles the Doctor, Ace and Benny aboard the transport taking the skiff to Corman, and on the way, the Doctor explains that the Tzun are genetic warriors; they conquer other worlds in order to transform their inhabitants into Tzun hybrids, thus adding the new race’s unique abilities and skills to their own genome. The transport reaches Corman AFB, but as the Doctor emerges from hiding Stoker spots him -- and recognises him, although the Doctor has never encountered the Tzun in this incarnation before. The Doctor and his friends escape from their pursuers and shelter in Nyby’s office, where the Doctor finds evidence that Nyby is working with the Tzun; however, he also finds evidence that there is another, unrelated alien presence at work on the base…

The records in Nyby’s office indicate that the Tzun intend to attack the Elephant Butte power station, and that the warheads stolen from White Sands have been shipped to Washington, D.C. The Doctor sends Ace and Benny to deal with the warheads, while he and Davison return to White Sands, intending to continue on to Elephant Butte and try to contact the Tzun. Ace and Benny steal a Hercules transport, but the landing gear snaps away from the aircraft when Stoker tries to block the runway with another plane. As Ace ponders how to land safely, Benny discovers that the transport is carrying crates filled with Tzun disruptors; apparently Nyby believes that his allies intend to supply America with advanced weaponry with which to win the Cold War. Ace manages to convince the air traffic controllers at Washington’s National Airport that she requires an emergency runway clearance, and crashes the plane; she and Benny then flee as the plane goes up in flames behind them, destroying the Tzun disruptors.

Kreer and Stoker return to White Sands, where Finney becomes suspicious, eavesdrops on them and discovers that they have been consorting with aliens. They in turn catch him and implant him with an electronic control to prevent him from acting against them. When Davison and the Doctor return, Davison discovers Finney’s condition and has no choice but to take command. She is then invited by the producer of a local TV programme to appear on a round panel discussing UFO sightings and alien abductions, but Stoker prevents the broadcast from taking place, claiming that it would compromise national security. The Doctor witnesses Stoker’s intervention and questions one of the disappointed panelists, Robert Agar, who claims to have been given a message of universal brotherhood by the peaceful inhabitants of Venus. In fact, Agar was contacted by the Ph’Sor Tzun, genetically engineered human hybrids sent to convince the people of Earth that the Tzun come in peace.

The Soviets launch Sputnik, and the Tzun, identifying it as a primitive transmitter only, choose not to draw attention to themselves by shooting it down. Nyby is furious when he learns this, and realises that he can no longer trust his purported allies. Meanwhile, the Doctor learns that the saucer sightings began about five months ago, which would place them just after May Day. He has always wondered by the Russians did not launch Sputnik on their national holiday, and he now suspects that this did indeed occur -- but that the first Sputnik was hijacked by an alien intelligence which used it to summon the Tzun to Earth. The Soviets, embarrassed by their perceived failure, erased it from their records and claimed that this second, successful, launch was in fact the first.

Ace and Benny deduce that the Tzun have hidden one of their warheads beneath the Washington Monument. It is guarded by Ph’Sor Tzun, but Ace holds them off while Benny defuses the warhead. The Ph’Sor flee when human police arrive on the scene, and Ace surrenders to give Benny the chance to follow the fleeing Tzun back to their base. This turns out to be the Naval destroyer Jessup, which is moored at the Naval Research Laboratories, but when Benny boards the ship she is captured by Major Kreer -- who identifies himself as the Master. He recognises Benny from her published archaeological work in the 26th century, and realises that she has travelled here with the Doctor. He thus has her locked up, and then takes a moment alone to inject himself with the nanites which the Tzun have finally finished preparing for him; once they have restructured his genetic code, he will once more be a pure-blooded Time Lord with a full cycle of regenerations, no longer a Trakenite hybrid contaminated by the savagery of the Cheeta world. What the Tzun do not realise, however, is that he has also used their technology to build a Stattenheim remote control and summon his TARDIS to Earth. The Tzun have now outlived their usefulness, and he thus kills the two Ph’Sor who were to take the second warhead to Moscow, and replaces them with two hypnotised human pilots who will not deviate from their course for any reason…

Ace is interrogated by FBI agent Joe Manco, but uses the Doctor’s CIA connections to convince him that they’re on the same side. Manco has been investigating Major Kreer for some time, and when he shows Ace a photograph of Kreer, she recognises him instantly. Aware that Kreer has been spending a lot of time on the Jessup, Manco leads Ace to the ship to search for her missing friend, and they board the Jessup just as it leaves port. Manco tries to arrest the Master, but the Master kills him with his TCE, and in a fit of rage Ace shoots the Master through the chest as he flees to his TARDIS. The Tzun nanites have done their work, however, and once inside his TARDIS, the Master successfully regenerates. This means that nobody recognises him when he returns to Corman AFB, but this is no longer a major concern to him, as he merely hypnotises the few soldiers who pose a threat. Since Nyby and his men are no longer required, the Ph’Sor Tzun turn on them and lock them up to await the war which will soon break out. Meanwhile, Ace and Benny fight their way off the Jessup, and when Ace shoots a pile of Tzun disruptors as a distraction, the fire spreads, causing the ship to explode moments after they leap into the river.

The Doctor convinces the director of the Elephant Butte station that he is about to be attacked by rogue American military officers using an experimental new plane. Andrews thus allows the Doctor to rewire the power grid to generate an EMP, and is startled when this causes an alien spaceship to appear from thin air and crash nearby. The Doctor finds to his sorrow that the crew of the skiff killed themselves rather than permit the humans to capture them. Nevertheless, he pilots the skiff into orbit to contact the leaders of the invasion force. On a mile-long Stormblade mothership, the Doctor meets Councillor Shok’Arl, who reveals that the Master called the Tzun to Earth, as he needed their help to escape and cure his genetic disorder. The Ph’Sor have been contacting individual humans with a message of universal brotherhood, while the Master has arranged to detonate nuclear warheads in Washington and Moscow. This will wipe out the planet’s two most powerful governments and trigger a nuclear exchange which the Tzun intend to stop, believing that the humans will welcome their saviours with open arms.

The Doctor, however, reveals that the Master has imposed press blackouts and discredited the Tzun’s contactees; their message of peace has not reached the human race, and their arrival will be greeted with fear and suspicion. Humanity may even blame them for the nuclear exchange, and entrench themselves on Earth in a state of xenophobic shock from which they may never recover. The Tzun investigate and determine that the Doctor is telling the truth, and, much to the Doctor’s surprise, they choose to give up the Earth as a lost cause and depart in peace. As they prepare to leave, they transport the Doctor back to Corman AFB to deal with the Master, and also transport Ace and Benny directly there from Washington to help him. Stoker is ordered to arrest the Master, but the Master reminds him of the photograph he saw earlier, and reveals that Stoker is a flawed first-generation Ph’Sor, grown from cloned human tissue and subject to inappropriate emotional outbursts. The Master claims that his fellow Tzun intended to dispose of him and his fellows once their purpose had been served; but if Stoker helps the Master, he can bring a new vitality to the Tzun Confederacy. Stoker throws in his lot with the Master, and he and his fellow Ph’Sor turn on the second-generation Ph’Sor who remain loyal to Shok’Arl.

Benny releases Nyby and his men, who begin to kill all aliens in the vicinity, regardless of their allegiance. In the confusion, Ace tracks down the Master again, but he takes her gun -- and gives it to the Doctor, challenging the Doctor to shoot him through the hearts and end his life. The Doctor is unable to do so, but he and Ace escape before the Master can kill them both -- or so they think. In fact, the Master has allowed them to escape. The Doctor gets to the telemetry unit which guides Tzun skiffs through the gravimetric disturbances in the Earth’s atmosphere, and shuts it down -- just as the Master had planned. The Doctor has now outlived his usefulness, but fortunately, the Master had not figured Benny into his plans, and she rescues the Doctor and Ace as the Master sends the Ph’Sor to kill them. The Doctor then takes his companions back to the TARDIS to track down the plane taking the second warhead to Moscow.

Stoker realises too late that the Master, while telling the truth about his genetic heritage, lied about the Tzun’s intentions; in fact, they intended to correct the genetic defects in Stoker’s kind rather than simply killing them. By now, however, Stoker’s rebellion has caused enough chaos to serve the Master’s purpose, and the Master therefore kills him and launches one of the evacuation skiffs on remote control. Due to the loss of the telemetry unit, the Tzun see nothing unusual about the empty skiff’s flight path, and allow it to dock with the Stormblade -- and as soon as it’s on board, the Master detonates a bomb in its engines, triggering a matter-antimatter chain reaction which destroys the Stormblade and all of the thousands of Tzun aboard. Before departing, the Master contacts the Doctor to tell him what he’s done, and the horrified Doctor realises that the Master simply lured the Tzun here to provide himself with a cure for his own genetic disorder, and then disposed of them as if they were no more than tools which had outlived their usefulness.

The Doctor locates the American plane as it enters Soviet airspace, but the Master has booby-trapped the second warhead; if the TARDIS materialises around it, it will explode immediately. To save the Earth it appears that the Doctor will have to sacrifice his TARDIS, but instead he manages to modify a Tzun disruptor which Ace had confiscated from one of her attackers and uses it to disintegrate the warhead without touching it. He, Ace and Benny then get the plane’s hypnotised pilots into the TARDIS and flee, moments before the plane is shot down for violating Soviet airspace. The Doctor returns the pilots to White Sands, where Finney is recovering from his ordeal; Davison has led a team to Corman AFB and has arrested Nyby for conspiring with unallied forces. There are apparently no more Tzun on Earth, and Ace chooses not to mention that tricking an alien species into attempting to invade another world in order to plant a trap and dispose of them is something that the Doctor has been known to do himself, on occasion.