Susan can still hear the sound in her nightmares sometimes and it’s so loud it wakes her up. She can also hear the voice of the man who died all those years ago, although she can’t be sure if she’s actually hearing it or just imagining it. Hearing that sound marked the moment when she first realised she’d have to leave her grandfather behind and make a life for herself. She was only an accidental passenger, a hanger-on, but he was spending so much time protecting her from the terrible things in the Universe that he wasn’t able to experience its wonders for himself.

Susan realises that if she wants to stop the nightmares, she’ll have to write them down and get them out of her head. It’s not fair on her husband as he doesn’t understand all the things she’s seen. He still thinks of her as human and it’s easier for both of them if she lets him carry on thinking that. She thinks back to the time when Ian and Barbara were travelling with her and her grandfather in the TARDIS and they’d started to feel like an extended family. They’d stopped thinking of her as a schoolgirl, although they didn’t realise she was already older than them put together. And yet, although the Doctor looked old, he was no more than an adolescent as far as their own people went, and Susan was just a baby!

The TARDIS was shaken by a terrible sound, like someone had just stabbed the Universe and it was crying out in pain. The Doctor checked the controls as if he knew what he was doing, but Susan knew it was mainly an act he put on to impress Ian and Barbara. He was still learning about the machine and the entire navigation system was still a mystery to him. He had yet to establish the mystical bond with the TARDIS that their people were supposed to have, so he still made mistakes.

The Doctor said something was sending shock waves through the space-time continuum and he didn’t think it was a natural phenomenon. The TARDIS landed, but as Ian and Barbara stepped outside, the Doctor seemed to be afraid and it looked as though he might close the door and leave them behind. Outside the TARDIS they could smell ozone and the rich damp of vegetation. They were amidst a tangle of vines, bushes and tree trunks, but the floor was metal and beyond the forest was a metal wall. The Doctor concluded there were on a spacecraft and said the leaves were vibrating in tune with some kind of space drive. Ian thought they could be in a hydroponics section, with the plants providing oxygen for the crew. Susan found a path through the vegetation, so they set off in search off to explore. The Doctor was keen to find the source of the noise as he thought it’d sounded too powerful to be safe.

They hacked their way through the undergrowth, detouring whenever it became too thick. Occasionally they’d find a door or a bulkhead made of a blue metal. It was like being in a tropical greenhouse. Barbara discovered the leaves were turning to follow them as they moved, as though they were being tracked. They came to an arch leading into a larger room containing a control console which was completely overgrown with tendrils and leaves. They cleared them off, then Doctor said the panels displayed some kind of energy field that was building up to a catastrophic level. The vines began to move in to fill the gap they’d created - but then the tendrils actually started operating the controls. The plants pulled down one of the levers and the ship suddenly lurched, throwing everyone to the floor. The Doctor discovered the energy had been discharged and it was starting to build up again from zero. He estimated the next discharge would take place in less than an hour. This was only a subsidiary area with equipment separate from the engines and navigation system, so they needed to find the main control room and speak to the Captain of the vessel.

Ian suggested following the vines back to their roots. They moved through numerous corridors and hallways, but as they passed a half-hidden doorway, Barbara noticed the plants inside looked different. The leaves were brown and curled up, and they didn’t move like the other plants did. Ian pulled off a leaf and the Doctor admonished him, reminding him this was all part of a living creature. Ian pointed out that the leaf was dead, but the Doctor compared it to someone pulling out a handful of hair. They carried on walking for ages, noting that the entire ship was interconnected, presumably to enable the vines to grow everywhere. The air was heavy with water that was sprayed from nozzles in the ceiling and down into gratings on the floor. They found several other corridors where the plants were dry and brittle and the floor was carpeted with dead leaves. It was clear the ship was designed to carry the plants, but something had obviously gone wrong.

Eventually they found the bridge. It was a huge hall with a vaulted ceiling festooned with greenery and the walls were lined with display screens and controls, with vines curled around each button and lever. The far wall contained an enormous viewscreen looking out to space. Hanging from above, like a vast chandelier, was a trunk-like swollen mass of bark, moss and roots, with vines leading away through every doorway to the rest of the ship. The Doctor realised this single plant was both the Captain and the crew! He introduced himself and the plant responded by rustling its leaves to create a voice. It gave its name as Rostrom and said it was concerned that it had no memory of their arrival. Barbara thought this might be because the plant was damaged and she explained about the areas where the leaves were dying. Rostrom said it had begun to suspect parts of its being were dead as there were areas of the ship that were closed off to it now.

Barbara found a nameplate on the wall that said the ship was Earth Benchmarking Vessel Nevermore and that Captain Rostrom was an artificial vegetative lifeform. The Doctor was intrigued and said he had no idea genetic manipulation was so far advanced in this era. Rostrom said it had been 338 years since his species was created by humans to crew their vessels and free their time for other things, like sculpture and music. The plants were designed to pilot the ships between the stars, move cargo and take passengers, fight the occasional small war and push back the boundaries of the human empire. As a new race, there were still some genetic quirks and anomalies that needed to be worked on. Some of them had suffered from parasites that killed off leaves and branches and some had been poisoned from the metal in the hull.

Barbara asked Rostrom if it ever got bored without someone to talk to, but the plant laughed at her. It said vegetables thrive on boredom and within its genes were 100 million years of doing nothing but reaching for the Sun and opening and closing its petals. It was evidently unhappy that the travellers had intruded on its calm routine and asked why they were here. The Doctor said their journey had been interrupted and that something on this spacecraft was damaging the space-time continuum. Rostrom said this was due to the Benchmarking activity and explained that it was a simple navigational process. Barbara likened it to what the English and Spanish navies did in the 17th century - it was no good explorers simply heading off blindly in the direction of the horizon as they’d soon be knocked off course by winds and currents. Rostrom said there were gravitational currents in space too and you couldn’t just head towards a particular star, because that’s simply where the star was located hundreds of thousands of years ago. The answer was to make sure you knew what the exact time was at both your destination and on your ship, then work out the time difference between the two. Benchmarking worked by using gravitational singularities to punch holes in the fabric of space every tenth of a light year, then they encoded into each hole information about how far it was from Earth and in which direction the ship was heading. The Nevermore was the first of such ships, but there would be many more, and once they’d finished, they’d have a grid that expanded the entire galaxy so spaceships would always know where they were.

The Doctor said the idea was monstrous. He accused Rostrum of interstellar vandalism and pointed out the dangers inherent in such a scheme. He said the fabric of space-time was weaker in some places than in others and you simply couldn’t go around cutting holes in it. Rostrum assured him the theory had been proven to be safe, but the Doctor insisted there were ’things’ living in the deep space beneath space, like the sea monsters that sailors used to fear - but in this case they were real. He said the creatures rarely come to the surface, but if holes were punched through into their domain, it would create avenues for them to use to enter our Universe. He demanded Rostrum stop the process immediately and they began to argue furiously. Neither of them were willing to back down and as Ian and Barbara tried to calm them both, Susan got bored and wandered off.

Susan was happy to explore the ship alone now that she’d met the Captain and the mystery had been solved. She soon found more areas where the leaves were dead and the tendrils were brittle. Eventually she came across the ship’s engine room and, to her surprise, she found a human working on the vast machines. The man told her she shouldn’t be here and asked how she got on board. Susan explained what had happened and the man was intrigued to hear that her grandfather thought the Benchmarking process was dangerous. He said the problem was that humanity treated mathematics like art and if an equation was beautiful and symmetrical, they believed it must be true, but in reality something beautiful could be a lie and something ugly could be true. Susan suddenly felt very hot and the man told her she should leave as there were energies in this room that could be harmful if she stayed. She wondered why anyone would build a spaceship that could cause harm and the man said he’d been thinking the same thing. Susan started feeling a tingling sensation along her arms and shoulders, so again the man urged her to leave. He said he was used to its effects and told her he was a traveller himself and was only here temporarily. He seemed disappointed that she always agreed with her grandfather and told her she should make her own decisions or else she’d never make any progress. She said she and her grandfather needed each other, but he said that by wandering off on her own, she was obviously ready to make up her own mind whether she realised it or not. He said people shouldn’t spend the rest of their lives following someone else and they had to take responsibility for their own actions.

Suddenly the entire ship began to shake. For a moment Susan thought it was the Benchmark process punching another hole in the Universe, but this was different. The man said it sounded like something had blown up and he discovered an area had been sealed off by air-tight doors to prevent the atmosphere leaking away. He said the ship was surprisingly fragile and it couldn’t take much more damage like that. Susan asked if Rostrum could repair the damage, but the man said it might not be able to sense it if bits of its body were dropping off all over the place. He agreed to stay and monitor the situation while Susan went back to tell the Captain.

Susan was convinced there was no way they’d be able to survive the impact of the approaching missiles, but then suddenly space itself seemed to rip open from a point near the Nevermore to a point infinitely far away. There was a flash of impossible light, made up of colours nobody had ever seen before, and then something squeezed through the gap. They saw tentacles made up of glowing energy which wrapped themselves around the alien spaceship and dragged it back into the fissure. Smaller tentacles then did the same with each of the missiles.

Everyone looked at the screen incredulously and wondered what had happened. The Doctor explained that this was one of the monstrous beings that lived beneath space, always hungry and always alert. Thanks to the Benchmarking, it’d been able to break through into normal space. They picked up a distress message coming from the other vessel and listened as the other captain warned that his ship had been destroyed while engaging a belligerent enemy vessel that had been sabotaging space around their major trade routes. The alien captain believed they’d been attacked by the Nevermore and accused them of a deliberate act of aggression. He warned any nearby forces that their space was being invaded, then he screamed…

Susan realised the captain had simply been protecting his borders from what he thought was an act of aggression. She accepted that it shouldn’t have opened fire on them, but then perhaps the Nevermore shouldn’t be going around opening up holes in space near other people’s star systems. The Doctor turned on Rostrum again and told him his actions were not only dangerous to the fabric of the Universe, they were also inflammatory to other races. Rostrum said they’d assumed other people would be grateful as they too would be able to use the process to aid their own navigation. The Doctor said space here had just frayed apart and it probably ran all the way to the last Benchmark. Ian wondered whether this area could be cordoned off, but the Doctor said any small disturbance might cause another rip between two holes and the problem could escalate with more and more rips forming until a whole section of space detached and floated away, leaving the creatures behind to feed at their leisure.

The Doctor told Susan there was a possible solution - he might be able to use the immense power from the TARDIS’s time engines to heal the fissure, but he was worried it would destroy the TARDIS. They’d be left here without a means of transport, stuck in one time and place forever. Susan argued that at least they’d have saved the Universe. The Doctor returned to Captain Rostrum and they started arguing again, and when Ian and Barbara stepped in to act as peace makers, Susan decided to find the crewman she met earlier to see whether the engines could be repaired.

Susan found herself in an area of the ship she’d never seen before. Large power cables fed into spherical tanks the size of a small asteroid. Once again, Rostrum’s leaves and vines were dying and Susan began to wonder just how widespread the problem was. The crewman appeared and told her she had a habit of wandering into areas she shouldn’t be. He told her this was the place where the gravitational singularities that trigger the Benchmarking were stored. Each of the seven tanks contained one singularity, trapped inside a magnetic Klein bottle. By dropping the magnetic field briefly, one of the singularities would momentarily plunge through the skin of things like a needle, then the singularity would be pulled back when the field was re-established. Meanwhile, the other six singularities would inscribe gravitational information on the boundaries of the hole, so that any traveller who used the Benchmarks would know where they were.

The crewman told her his position here was only temporary as he liked to move around a lot, clearing up messes and getting involved in dangerous situations. Susan thought he sounded very much like her group and asked if he had his own ship. His answer was a bit vague so she told him about the Doctor’s plan, adding that they were risking their own ship. The crewman said Captain Rostrum could take them somewhere safe and Susan thought the Doctor might even be able to build another TARDIS eventually. Susan said she’d go mad if she had to stay in one place as she wanted to experience the Universe, not just observe it from a distance. The crewman told her it would be impossible for her to go with him, but he could probably drop her off somewhere. She asked if he ever got lonely, but he said there’s a difference between being alone and being lonely. He said he was sure she could look after herself and that she didn’t need a grandfather figure to fall back on, but she was scared by the prospect of heading off on her own.

Susan started to look unwell again, so he suggested she return to her friends. Before she could do so, she cried out and collapsed. She pleaded with the crewman to help her, but he said he couldn’t and walked away! Susan couldn’t believe he’d left her and she tried to call after him, but she couldn’t make a sound. She wondered if she was suffering from the same thing that was affecting the vines and the leaves? She drifted in and out of consciousness and was only woken up when Barbara came rushing over after getting worried that she’d been gone so long. Barbara helped her to her feet, but when Susan asked her what happened to the crewman, she said she hadn‘t seen anyone.

By the time they returned to the bridge, Susan was almost back to normal. The Doctor was still intent on staying behind and using the TARDIS to repair the fissure, and she just hoped that their sacrifice wasn’t going to be in vain and that another Benchmarking ship wouldn’t come along soon and cause the whole problem again. Ian was struggling to understand the concepts and kept coming up with analogies that just confused him even more. Barbara turned furiously to Rostrum and told him off for letting one of his crewmen walk off and leave Susan unconscious on the floor. The Captain assured her he had no crew and that he was alone on this ship. Susan said she’d talked to the man twice, but when Ian asked her what his name was, she realised she didn’t know.

The Doctor guessed they had another intruder aboard, but Rostrum suspected he was one of their group, engaged in sabotage while they were distracting him. The Doctor pointed out that Rostrum had eyes everywhere, but Barbara reminded him some of the leaves and branches were dying. Ian asked Susan whether the leaves were alive or dead in the areas where she met the man and she realised they were dead in both cases. Ian thought the man might be taking advantage of those areas to creep around, but the Doctor suggested he might have deliberately caused the dead areas himself to cover his tracks! He turned to Rostrum and asked for maps of all the areas where the plant no longer had any senses. Rostrum was suspicious, but the Doctor pointed out that the stranger was undoubtedly hiding in those areas. The group decided to split up and each of them would search the areas one by one. Barbara suggested Susan stay behind as she was still unwell, but Susan refused to be treated like a child any more. The Doctor looked at her curiously, as if he’d suddenly realised she was growing up, and it didn‘t seem like he was entirely comfortable with the idea.

Susan already knew where she’d seen the mysterious crewman before, so she knew roughly which areas of the ship he’d been working on. Spreading out from there, it wasn’t long before she found him, standing in the control room, not far from where the TARDIS had originally landed. He was pulling the lever that operated the Benchmarking process and she noticed the nearby tendrils had all turned brown and twisted. Susan realised it was him who was killing the plant and that everywhere he went, the leaves and vines were literally dying. He argued that the plant was killing so many others through its actions. He told Susan they were opposites of each other and he warned her not to get too close. Susan became weak again and had to sit down. He revealed that he was draining her life away just as he was doing the same to the plant. It wasn’t through choice and he didn’t want to be responsible for her death. She realised he wasn’t human and told him she’d keep following him until he told her what he was doing here, even if it killed her.

Ian and the Doctor suddenly leapt out from a side corridor and attacked the man, pulling him down to the ground. They quickly dragged him to the storage area where they could restrain him, but both Ian and the Doctor were starting to look pale so they had to take turns while the other rested. Simply standing at a distance for a couple of minutes seemed to be enough for them to recover their energy and after a while, Barbara joined them and helped out. As they moved down several corridors, the leaves and vines they passed started to wither and die, then they gradually recovered again after they‘d moved on. Eventually the intruder was tied up and locked safely away. It only now occurred to Susan that the man and the Doctor both looked very much alike. They were both old and white haired and they were both quite imperious in their looks and attitude. Yet, there was something softer about the intruder that she rarely saw in her grandfather. The Doctor suspected the man had some sort of connection with the fissure outside the ship and wondered if he knew a way of fixing it.

The Doctor and Susan decided to question him and they stood on either side of the room to avoid getting too close. The man confirmed that he was from the other side of the fissure and said they had to free him or else the most terrible things would happen. The Doctor believed only monsters lurked beneath the surface of space, but the man laughed and said that’s what his people said about this side. Of course, in his case, his people believe they’re living on the surface and this space is underneath. The Doctor was surprised to discover there were civilisations there, including intelligent ethical life, but the man says it didn’t really matter which side of the divide you lived on. His race were formed of different patterns of energy and different structures of matter, which is why when he took on human form, he based it on an image he picked up from Susan’s mind. He added that because they’re opposites, his physical presence was draining their life, and if they were to cross over to his realm, they’d do the same to his people.

The man revealed that the actions of this ship had been causing great distress to his people. Vast tracts of space have been lain waste by the effects of the Benchmarking, so he came here to stop it. He was prepared to use force if necessary, but he’d prefer to use guile or even just intelligent conversation. The Doctor announced that they’d help him and told Susan to release him so they could escort him to Captain Rostrum.

Suddenly they heard Ian calling for help, saying that he and Barbara were held fast in Rostrum’s vines. The voice of Rostrum boomed out, claiming they’d betrayed him and that he knew they were all working together to sabotage his ship. He insisted the Benchmarking would continue and said they’d stay here as his prisoners and rot for as long as it took him to complete his mission. Ian pleaded with the Captain to think logically and pointed out that their presence had no effect on the plants so they couldn’t be working with the intruder. Unfortunately the Captain had never seen or felt the presence of the intruder and he only had their word that the man even existed. The Doctor reminded the plant about the catastrophic dangers inherent in the process, not only in the Universe but the other one too, but Rostrum refused to believe his words.

The Doctor asked the intruder for his assistance and the man said he knew enough about the way Benchmarking worked to seal the fissure, but he needed to return to his original form in order to do it. Susan urged him to do it, but if he changed form right now he’d kill every living thing within half a light year. Susan urged him to do it anyway and not to worry about them, but the Doctor said the TARDIS sat outside time and space and they’d be safe inside there if they could make it. Unfortunately Ian and Barbara were captives of Captain Rostrum and he’d never let them go. Susan asked the intruder if he could change his form slowly enough to weaken Rostrum’s binds and allow them to escape before they were harmed. He wasn’t sure if he could hold it back so long, but he agreed to try.

The man’s body began to glow and shift. Susan was worried that healing the fissure would require all of his power and prove fatal to him, but he told her to leave immediately. The Doctor and Susan ran from the area as the man’s body transformed into light, darkness and chaos. Ian managed to pull Barbara free from the vines and then together they all staggered back to the TARDIS. They were on their hands and knees when they arrived and the Doctor dropped the key. He was too weak to pick it up, but Ian found it and they managed to get inside.

They stayed in the TARDIS for hours, recovering their strength. When they eventually emerged, they found Captain Rostrum was dead, but on the viewscreen there was no sign of the fissure. The man had sealed it with his life. Ian wondered what would happen to the Benchmarking ships and the Doctor said he hoped humanity would learn its lesson, but he doubted they would. Susan noticed a flashing light on the control panel and thought Rostrum had recorded a final message before he died, but when they played it back, it turned out to belong to the alien man. He was calling out an emergency to all civilian and military forces. He said he’d been fatally injured while repairing damage done during an innocent encounter with a vessel from the other side of the spatial membrane. He said the vessel had accidentally weakened the fabric of space around their major trade routes, but when he confronted the occupants they showed great courage in assisting with halting the damage. He said they weren’t the monsters they’d always believed, but all further contact should be avoided as their essential natures couldn’t co-exist.