Benny is on holiday on a lovely Earth colony, in theory. In practice, the continents of Pevena and Calabraxia are at war, and the map which her travel agent gave her is only useful if she doesn't fall asleep at the tiller of her yacht and drift into enemy territory without noticing. She's been shot out of the water, she's been stuck on a desert island for two days, she's run out of food and water, she knows she's going to die, and she's already started hallucinating. Either that or the captain of a 17th-century sailing ship really is offering to rescue her. Benny considers the probability of this really happening, and decides to pass out. The ship's sole passenger, General Hannah Brennan, insists that they continue on, but the Cassandra is making good time and Captain Damien Colley refuses to leave Benny. He's been at sea too long just to abandon someone to the elements, and if Brennan insists that they do so, then he'll abandon her on the island instead. Brennan is furious, but realises that she has no choice. The Cassandra has just acquired another passenger.

Benny awakens aboard the Cassandra and realises that it's for real, sort of; the ship is in fact a high-tech vessel with a working engine and an AI navigational system, and the sails, rigging and wooden decks are pure affectation on Colley's part. He takes Benny to her guest cabin, which to her exhausted eyes seems larger than the island she's just been rescued from, and gives her a communicator so she'll be able to contact him if she needs anything. As the Cassandra is fully automated, there are no other crew members, and Brennan is the only other passenger. As Benny refreshes herself for dinner, Colley returns to the bridge, where he finds that Colley has tried and failed to override the navigational systems and change course to get home more quickly. The Cassandra's AI, which refers to Colley as its dad, refuses to alter its course; there's a storm ahead, which must be avoided. Brennan accuses Colley of risking their mission by bringing a woman of unknown loyalties aboard, but Colley points out that running a force seven storm at full speed is even riskier...

Dinner takes place in strained silence. Brennan fears that Benny is an enemy spy, and Benny's attempt to break the ice by jokingly claiming to have poisoned her doesn't go over very well. The infuriated Brennan accuses Benny of following her from Glory Hill, but then suffers from a sudden migraine and must retreat to her cabin to rest. Colley explains that this voyage will ensure the end of the war, and the stress is causing Brennan to see enemies everywhere. He won't say anything further, as he's seen too many people die to want to put Benny in danger. This is why he opted out of the war himself; although Brennan doesn't know it, Colley works for both sides, ferrying cargo and passengers for both the Calabraxians and his own people, the Pevenans. He and Benny take a stroll around the deck after dinner, but their voices carry to the cargo hold, where his other passenger hears Benny and questions Brennan about her. Brennan ignores his questions and simply gives him more food; he may be caged up, but she doesn't want him starving before they reach Calabraxia and she can get what she needs from him...

The next morning, Colley goes to the bridge, to find that the storm front has moved; they're currently sailing ahead of it. Cassandra reports that Benny is using the computer terminal in her cabin, and Colley, who doesn't wish to spy on her, tells Cassandra to allow Benny to access any system she wants. As he prepares breakfast, however, Brennan enters Benny's cabin and attacks her; she's convinced that Benny is a Pevenan spy, here to prevent her from taking her prisoner to Calabraxia. Benny wakes with a headache in the cargo hold, where she sees that Brennan is also suffering from a much more severe headache -- and that a man named Sheen is caged up in the hold. Cassandra locates Benny by monitoring her brain waves, although it takes her some time to locate Brennan, who seems to be suffering from some sort of synaptic interference. Despite her migraine, Brennan insists that Benny be held prisoner as well, but Colley refuses, and sends Benny to the bridge to wait while he talks sense into Brennan.

On the bridge, Benny is surprised when the AI responds to her private musings, and speaks of Colley as its dad. Cassandra then detects a Pevenan vessel nearby, and when Colley arrives, Benny suggests telling them about the prisoner. Colley refuses, and Benny assumes that he's just protecting his profits and doesn't care that Sheen is obviously going to be tortured. But there's more to it than that; Colley is sick of the war and wants it over. His daughter, the real Cassandra Colley, was a brilliant neurotech designer, who designed the onboard AI and programmed it to think of Colley as its father. She could have achieved so much, if only she hadn't joined the military and died in the Calabraxian attack on Glory Hill... The shock and loss killed Colley's wife slowly, and now he just wants it all to end. And as soon as Sheen arrives in Calabraxia, it will. Cassandra reports that the interference around Brennan's brainwaves is increasing, and that the general has in fact lost consciousness. Colley leaves to see to her... and as soon as he's gone, Benny questions Cassandra, and learns that Colley ordered her to let Benny access any system she wants. She thus uses the communication system to contact the Pevenan ship, and tell them of the prisoner.

Brennan is surprised to find Colley caring for her; however, just because he doesn't like her, that doesn't mean he enjoys seeing her in pain. He advises her to rest, and she must, although she fears that Benny's presence puts her mission at risk. She's right; even now, Benny is in the hold, trying to free Sheen. This is complicated by the seriously solid lock, and the fact that for some reason Sheen doesn't seem to want to escape. Cassandra hears Benny talking, deduces the problem and uses one of her defense lasers to blast open the lock... but she has no idea to whom Benny was speaking. Benny takes Sheen to the deck and tells him to wait for the Pevenan ship to emerge, while she goes to the bridge to contact the Pevenans. She is unable to do so due to some sort of interference, more than can be explained by the storm. Cassandra is more concerned by the man on deck; Colley had deactivated the security cameras in the hold, and Cassandra was unaware that there was anyone on board. Now he is visible on the monitors, but there is still a confusing sensory conflict regarding his presence. Before Cassandra can explain further, Colley and Brennan arrive, and Brennan furiously tries to take her prisoner, all of her fears apparently justified. But Cassandra then reports that the man on the deck has powered up one of her staser cannons...

Colley, Benny and Brennan rush out to the deck, but are too late to stop Sheen from firing on the approaching ship and blowing it out of the water, killing hundreds of his own people before they can rescue him. Brennan thinks he's gone over the edge and doesn't know who the enemy is any more, but that's not the case. He informs her that he's had enough of her incompetence and is no longer to be considered her prisoner, and when she protests, he single-handedly lifts her a foot off the deck. When she looks into his eyes she faints dead away, with another stabbing migraine. Benny, furious, demands to know what's really going on, but Colley just tells her to stay in her cabin, where she'll be safe. As Benny storms off, Colley assures the suspicious Sheen that she's just a stranded tourist, and that she won't trouble them from now on.

He clearly doesn't know her very well. Benny slaps Brennan awake and demands answers, as even the general must now know that Benny isn't the real threat here. Brennan reluctantly admits that she worked undercover at Glory Hill for over a year; Calabraxian intelligence slipped her in after the attack, having killed dozens just so she could blend in more easily. Sheen was the head of a project to develop a superweapon capable of destroying the entire Calabraxian continent, but Brennan kidnapped him and is taking him to Calabraxia for interrogation. Her only motive is to save her own people -- but why is Colley helping her, when he has good reason to hate the Calabraxians for killing his daughter at Glory Hill? And why is Sheen determined to get to Calabraxia as well? All is not as it seems, and Brennan is going to have to work with Benny to discover the truth...

Colley determines that Benny has not altered the navigational systems, but due to the changing storm front their course has changed; their ETA is now only 13 hours away. Sheen can tell that Colley is having second thoughts about their mission, but it's too late to stop now. Colley escorts Sheen back to the hold, intending to lock him up again, and once again orders Benny not to interfere. However, Benny uses reason to get through to Cassandra, who admits that her dad is behaving strangely. Cassandra therefore keeps an eye on Colley while Brennan breaks into his cabin and sorts through his meagre belongings. She finds a photograph of Colley, his wife and his daughter, and recognises Cassandra from a photograph in Sheen's office at Glory Hill... but before she can remember any more, another migraine causes her to pass out. Before rushing off to her aid, Benny asks Cassandra where Colley and Sheen are, but Cassandra reports that she is still experiencing sensory conflict. Her dad is in the cargo hold, but she can't detect a synaptic signal from Sheen at all.

The lock to Sheen's cage is beyond repair, but Sheen decides that this isn't important; Brennan can't stop him, thanks to what Glory Hill did to her, and if Benny interferes again then she will have to be killed. As Sheen and Colley return to the bridge they hear Brennan screaming in pain in the distance, and Colley is surprised when Sheen admits that he's responsible for her "migraines". She knows the truth about Sheen, and they had to erase that from her mind; the pain is caused when she tries to remember. As long as she's in this condition, nobody can stop Sheen from reaching Calabraxia, and wiping the continent from the face of the planet...

Benny gets Brennan back to her cabin, where she realises that the general's migraines must be related to Sheen; they seem to be triggered whenever she looks at him, or even remembers him. And yet she worked alongside him at Glory Hill for over a year, with no ill effects; the pain only started after she tranquilised him and fled from Glory Hill. The general's seizures get worse as she tries to remember, and Benny urges Cassandra to help. Cassandra is unable to detect any external sources causing the interference in Brennan's brainwaves, and thus starts to scan the general's brain itself. Benny leaves her to it and confronts Colley and Sheen, demanding to know the truth. This time, Sheen decides to reveal it. Colley is just weary and waiting for it all to end, but Sheen is triumphant -- for his eyes are covered in cataracts, a side-effect of the operation that turned him into the walking, living bomb which will destroy Calabraxia in ten hours' time. As Benny tries to absorb this, Brennan arrives, feeling better than she has in days; Cassandra has successfully removed the chemical blocks from her mind. Now Brennan remembers everything -- not only what Sheen is, but who he was...

As the furious Sheen attacks Brennan, Colley admits to Benny that he's acting to avenge his daughter's death. He couldn't leave Benny to die of exposure, and had hoped to drop her off somewhere on his way, but the storm rushed them to Calabraxia ahead of schedule. But a simple apology isn't enough for Benny; Colley's weakness in the face of personal loss is about to lead to the deaths of millions, and she can't forgive him for that. Sheen beats Brennan nearly to death, but allows her to live so she can watch the end of it all. With his triumph imminent, Sheen finally reveals the rest of the truth... he, Sheen, is Cassandra Colley. She always knew that the Calabraxians wanted either her knowledge or her death, and before the attack on Glory Hill, she transferred her mind into Sheen's manufactured body, so she and her team could keep working on a weapon to end the war while the Calabraxians thought her dead. Colley is stunned; he can't believe Cassandra would hurt a fly, let alone commit genocide. But Benny points out that Cassandra chose to join the military and work at a research centre, designing weapons of mass destruction, of her own free will. The captain didn't know his daughter as well as he thought he did.

Sheen proves what "he" is saying by dropping the blocks on his own mind; finally, the ship Cassandra is able to detect his brainwaves, and confirms that "Sheen" is in fact Cassandra Colley. Unable to deal with this revelation and with Sheen's clear contempt for him, Colley pulls out a gun and shoots Sheen, too upset to remember that Sheen is a living bomb set to go off within hours. As Sheen's heart starts to fibrillate, Cassandra detects a chemical change occurring within his brain; the bomb is about to go off. It will take too long for Cassandra to unpick the neural locks in Sheen's mind, but there's another way; Cassandra's and Sheen's AI networks were designed by the same person, and on similar templates, and Cassandra thus uploads her own intelligence into Sheen's body. Once his neural net is stabilised in its new pattern, the safeguards in his body switch off, and Colley gets him to the medical bay, where his condition is stabilised.