Benny and Ace discuss where they would like to go next, and convince the Doctor to take them to the moons of the gas giant Lucifer in the early 22nd century. A human expedition has come to Lucifer to learn the secret of the stable heavy elements in the planet’s core, but five years after their arrival they are no closer to solving any of the planet’s mysteries. The hollow moons Belial and Moloch orbit impossibly close to Lucifer, and are connected by a Bridge of woven microfilaments which should have snapped long ago under the tidal pressure. Belial is filled with incomprehensible technology, and Moloch with vegetation which, although untended for millennia, has not run rampant through the moon’s interior. There is life on Lucifer, but the “Angels” have ignored all attempts at communication, and nobody is sure whether it was they or another species which built the machinery in the moons. The obsessed scientist Alex Bannen demands that more funding and energy be allocated to the hard sciences, and that attempts to communicate with the Angels be abandoned -- but Paula Engado, the young daughter of the base co-ordinator, disagrees. Shortly after the TARDIS’ arrival, Paula makes an unauthorised attempt to communicate with the Angels -- but her starsuit malfunctions, dropping her straight into the heart of Lucifer to her death.

The grieving Miles Engado calls in an Adjudicator to determine the cause of Paula’s death, and Bishop arrives to find an expedition rife with inner conflict. The Doctor, Ace and Benny seem to have arrived from nowhere and have begun their own investigation into the death. Only Benny knew that Paula and Cheryl Russell were lovers, and now Cheryl’s husband Sam has vanished while checking out a malfunction in his own starsuit. Piper O’Rourke harbours unexpressed feelings for Miles, and is still bitter over the loss of her husband Ben; his ship, the Hydrax, vanished in deep space years ago, but since no body was ever found the company refused to pay out on his insurance policy. The base’s psychologist, Christine LaFayette, is overcompensating for her hatred of her mother, the CEO of the so-called “Holding Company” which controls every business interest on Earth. As Bishop begins his investigation, news reports start to come in of a mysterious black fleet which is attacking and destroying outlying human colonies; only the Doctor, Ace and Benny know that these are the first foreshadowings of the Dalek invasion of Earth.

Bannen shows the Doctor the “Mushroom Farm”, an assortment of metal structures in the centre of Belial, which seem to respond to the thoughts and emotions of the operator. Bannen believes he can crack the secrets of the Farm with more energy at his disposal, but Federique Moshe-Rabaan, the Islamic representative of the Energy Police, refuses to allot him any more than his fair share. The Doctor casually suggests a way in which the output of the expedition reactors could be increased tenfold and sets off in search of Ace, only to find that she has been attacked and nearly killed while trying to plant a message in the expedition’s intranet. She refuses to tell him what she was doing, and instead decides to visit Moloch on the Lift, a torus-shaped object which rides up and down the Bridge at irregular intervals.

Moshe-Rabaan is found dead with a vibroknife clutched in her left hand and a signed confession to Paula’s murder on her bed, but the Doctor knows that Muslims cannot use the left hand to hold cutlery; Moshe-Rabaan was murdered to throw them off the scent. Her death and the Doctor’s earlier comments give Bannen the opportunity he needs to power up the Mushroom Farm, but although he is able to activate the machinery he finds he is unable to control the resulting, runaway reaction. The moons begin to shift out of alignment and the Bridge tears apart, killing some of those on the Lift. Ace rallies the survivors together and they abseil down the interior of the Bridge to Moloch. The mechanisms of the Mushroom Farm turn out to be self-regulating, and once the Doctor stops the frantic Bannen from meddling, the damage begins to repair itself. In the confusion, it is revealed that Bannen is keeping a holographic simularity of his dead son Mark hidden away in the Mushroom Farm, and he admits to Piper that his wife and son were killed during the food riots in Mexico -- and that although he could have gone back for them, he chose to save himself instead.

Ace finds Paula’s video diary on Moloch, and after viewing it she contacts the Doctor in a rage -- but before she can reveal what she has learned, the sound of a weapons discharge is heard over the link and communications are cut off. Bishop takes a party to Moloch in his ship to investigate, and on the way, the Doctor watches the progress of the Lift and deduces that it and the Bridge supply the moons with energy, generated by the magnetic differential caused by the interaction of Lucifer’s outer atmosphere with the solar wind. Upon arriving on Moloch, the search party finds Ace’s discarded jacket atop a pile of bodies rendered unidentifiable by blaster fire. Bishop seizes Paula’s diary crystals as evidence, but the Doctor speaks privately with him before he views them -- and upon returning to Belial, Bishop arrests the Doctor for Paula’s murder.

The diaries seem to prove that the Doctor passed on a false message from Cheryl telling Paula that she couldn’t leave Sam, in order to manipulate Paula into making the voyage which led to her death; however, Bishop admits to Benny that the personality software he used to analyse the entry has provided seventeen possible motives for the Doctor’s action. A bomb then goes off in the conference room where the Doctor is being held prisoner, apparently killing him. Aware that Bishop had been monitoring the Doctor, Benny vows to force Bishop to reveal who planted the bomb -- but in so doing, she accidentally alerts the killer to the danger. The Doctor and Bishop had in fact been working together to lure the killer out into the open, but now she is aware of this and thus sabotages the neural net to prevent them from accessing the recordings and identifying her. Bannen discovers her doing so, however, and Piper thus attacks him and flees into the depths of Belial…

Miles, suicidally depressed and convinced that the spirit of Paula is haunting the base, takes a starsuit and attempts to copy her fatal plunge -- but as he falls into Lucifer’s atmosphere he sees what appears to be Paula’s spirit floating through the clouds towards him. She claims that at the moment of her death her spirit joined with that of a dying Angel, but refuses to explain any further, telling him only that he and his people must leave the Angels alone. Meanwhile, Ace awakens on a starship owned by the Interplanetary Mining Company, and discovers that the agent she’s been trying to contact is the ship’s captain, an alien named Legion who exists in seven dimensions. Earth Central has been forced to declare bankruptcy, and Project Eden has been seized by the Holding Company -- which has assigned Lucifer’s mineral rights to IMC. IMC’s fleet thus declares itself openly and seizes control of Belial, and the Doctor is shocked to see Ace at the head of the troops…

Legion rescues Miles from Lucifer and returns him to Project Eden, where the staff are shocked to learn that their severance packages do not include free passage back to Earth. Piper admits that she has been working for IMC all along; at first they strung her along with vague claims that they had learned the truth about her dead husband, and by the time she realised they were lying she was in too deep to get out. Seeing the way things were going on Earth, IMC ordered her to install a virus in the expedition’s neural net to give them access to its records and facilitate their eventual takeover -- but the shoddy programming of the virus caused the starsuit malfunctions that killed Paula and Sam. Legion claims that she is lying, and orders Ace to “terminate her contract”. Bishop protests, but is prevented from interfering by his direct superior, Bronwen ap Bryn -- who has accompanied the IMC fleet to Lucifer, and who informs the shocked Bishop that the Holding Company has declared the Adjudicator’s Guild an illegal organisation and disbanded it. Ace takes Piper out into the base’s corridors, but she is still uncertain whether serving Legion is the right move, and therefore lets Piper go.

The IMC troops burn away the vegetation in Moloch in order to explore the moon’s interior, and take the protesting Christine LaFayette back to their ship; her mother only gave birth in order to prove her power to circumvent the procreative lotteries, and she has no intention of letting her trophy daughter get away. Christine learns that Legion’s race has made a deal with IMC, supplying them with advanced technology in exchange for military supplies with which to defend themselves against the “Black Fleet”. Using controlled singularities supplied by Legion, IMC intends to strip away Lucifer’s outer atmosphere, clearing the way for exploitation of the heavy elements at its core, and incidentally killing all of the Angels. Ace locks Christine and Benny up on the IMC mothership, but they escape and get to a personnel transport, intending to join their friends at Project Eden. Before they can get clear, Legion unleashes the singularities, and Benny and Christine are caught in the gravity well of an incipient black hole.

Piper finds Miles boarding a shuttle with his tribe’s traditional medicine wheel, determined to enter Lucifer’s atmosphere and rescue his daughter. Piper accompanies him, and they find the Angels wheeling about the dying Paula. Paula once again tells her father that there’s nothing he can do to save her; the Angel she joined with was also dying. When the Angels die their bodies transform into the stable heavy elements which Project Eden first came to analyse, and with her final death Paula passes on one last gift, by transforming the medicine wheel into the same substance and thus giving Miles a sample to take back to Earth for analysis. As Piper and Miles try to return to Belial, they are nearly drawn up into one of the singularites -- but the singularities unexpectedly turn themselves inside out, and the Angels rise up to cluster around the radiant objects. Piper, Miles, Christine and Benny are suddenly transported back to Belial by the Angels, who tell the humans that they are not welcome in the Angels’ temples.

Legion has given Bannen freedom to continue his work in the Mushroom Farm, but Banne, realising that he’s just being kept out of the way while Legion gets on with what it considers to be its real work, decides not to reveal what he has discovered. Instead, he locks himself in the Farm, now confident that he can control its workings and restore the Earth to its state of purity. Legion, realising that things are getting out of control, orders Bronwen ap Bryn to expel all “non-essential” personnel onto Belial’s surface, killing them. When Bishop tries to stop her, Bryn prepares to shoot him, but Ace kills her first, saving Bishop’s life -- briefly, as Legion then kills Bishop himself. The Doctor, admitting that he is no less guilty for manipulating others into doing his killing for him, shoots and kills Legion. Ace admits at last that she tricked the Doctor into bringing her here, having been contacted by IMC in the 26th century. They had met the Doctor before, and, knowing that she had travelled with him, they told her that if he ever contacted her again, she should use him to find out why the Lucifer system became blocked behind an impenetrable barrier after their attempted incursion.

Bannen activates the Mushroom Farm, and waves of energy ripple out, randomly changing the very nature of the life forms they encounter. The Doctor sends the survivors of Project Eden to safety in Bishop’s ship, while the leaderless IMC troops scatter in disarray; however, for some it is already too late, as their lymphatic fluid turns to acid, their sensory apparatus alters to accept only radar input, their lungs become capable of metabolising only fluorine… The increasingly desperate Bannen manages to protect the Doctor, Ace and Benny as they rush to the Mushroom Farm, which the Doctor now deduces is an engine designed to rewrite the morphic fields of living creatures, transforming them on the most fundamental of biological levels. This is how the Angels transformed themselves into their current forms, and it how Bannen hoped to save the Earth -- but what he did not realise was that the forest inside Moloch was the stabilising mechanism, and that the IMC troops have destroyed it. The Farm can no longer be switched off, and this time, the damage that Bannen has caused will not repair itself.

The Doctor realises that since the Mushroom Farm is controlled by the emotions of the operator, Bannen will be unable to put matters right due to his own emotional traumas and insecurities. The Doctor, Ace and Benny combine their mental energies to bring the Farm under control, and Bannen, accepting responsibility for his actions at last, allows them to transform him into another living forest, to spend the rest of his life as the unit’s new control mechanism. The Angels then seal off Lucifer and its moons from the rest of the galaxy, unwilling to allow intruders to disturb them at their worship. The survivors of Project Eden are on their way back to Earth with the transformed medicine wheel, and with a gift of the Doctor’s -- a concoction which will confer a measure of immunity to the coming Dalek-generated plague, so that some of the Earth’s population survives to fight back. Ace decides to continue travelling with the Doctor, and departs with him and Benny, leaving the Angels to worship at the singularities while Bannen experiences peace at last.