LYRA HAD NEVER SEEN SO many houses or imagined that there could be so many people in the world. She knew the facts—she’d heard the nurses and doctors discussing them sometimes, problems with overpopulation, the division between rich and poor—and the nurses often watched TV or listened to the radio or watched videos on their phones when they were bored. But knowing something was different from seeing it: house upon house, many of them identical, so she felt dizzyingly as if she were going forward and also turning a circle; car after car lined up along the streets, grass trim and vividly green. And people everywhere. People driving or out on their lawns or waiting in groups on corners for reasons she couldn’t fathom.

Jake stopped again at one of these houses, and Gemma got out of the car. Lyra watched through the window as a girl with black hair emerged from the house and barreled into Gemma’s arms. Lyra was confused by this, as she was by Jake and Gemma’s relationship, the casual way they spoke to each other, and the fact that Gemma was a replica but didn’t know it. But she was confused by so much she didn’t have the energy to worry about it.

For several minutes, Gemma and the other girl stood outside. Lyra tried to determine whether this second girl, the black-haired one, was a replica or a regular human but couldn’t tell, although she was wearing human clothes and her hair was long. She used her hands a lot. Then the girl went inside, and Gemma returned to the car alone.

“April’s going to open the gate,” she told Jake. She sounded breathless, though she hadn’t walked far. “You can park next to the pool house.”

Jake advanced the car and they corkscrewed left behind the house. Lyra saw a dazzling rectangle of water, still as a bath, which she knew must be a pool. Even though she couldn’t swim, she had the urge to go under, to wash away what felt like days of accumulated dirt and mud and sweat. There were bathtubs in Postnatal, and even though they were too small to lie down in, Lyra had sometimes filled a tub and stepped in to her ankles after it was her turn to tickle, engage, and maintain physical contact with the new replicas.

When the gate closed behind them with a loud clang, Lyra truly felt safe for the first time since leaving Haven. Contained. Controlled. Protected.

Next to the pool was a miniature version of the big house. Sliding doors opened into a large carpeted room that was dark and deliciously cold. The house was mostly white, which Lyra liked. It was like being back in Haven. Goose bumps ran along Lyra’s arm, as if someone had just touched her. Where the carpet ran out was a kitchen alcove that Lyra identified only by its stove: it looked nothing like the kitchen in Stew Pot, a vast and shiny space filled with the hiss of steam from industrial dishwashers. Through an open door she saw a large bed, also made up with a white sheet and blankets and so many pillows she couldn’t imagine what they were all for. And lined up on bookshelves next to the sofa: books. Dozens of books, four times as many as she’d seen in the nurses’ break room, so many that in her excitement the titles blended together and she couldn’t make out a single one.

She wanted to touch them. Their spines looked like different-colored candies the nurses exchanged sometimes, like the sugared lozenges the replicas got sometimes when they had coughs. But she was almost afraid to, afraid that if she did they would all blow apart. She wondered how long it would take her to read every book on the shelves. Months. Years, even. Maybe they would be allowed to stay here, in this clean and pretty room, with the sun that patterned the carpet and the soft hum of hidden air-conditioning.

At W-A-L-M-A-R-T, Gemma had bought Lyra and 72 new clothes—“nothing fancy, and I had to guess how they would fit”—soap, shampoo, toothbrushes and toothpaste, and more food, including cereal and milk, granola bars, cans of soup she said she could show them how to heat in the microwave, and at least a dozen frozen meals. She showed them where the shower was—a single shower stall, the first Lyra had ever seen—and apologized that there was only one bed.

“So, you know, you’ll have to share, unless one of you wants to take the sofa,” she said. Lyra felt suddenly uncomfortable, remembering Pepper and her unborn baby, and how she’d been found with her wrists open; the Christmas parties when the doctors got drunk and sometimes visited the dorms late at night, staggering on their feet and smelling sharply of alcohol swabs. That was why it was better for males and females to stay apart. “I know you must be exhausted, so we’re going to leave you alone for a bit, okay? Just don’t go anywhere.”

Lyra didn’t bother pointing out that they had nowhere to go.

“Get some sleep,” Gemma said. The more Lyra looked at her, the less she resembled Cassiopeia and her other genotypes. That was the funny thing about genotypes, something the nurses and doctors, who could never tell them apart, had never understood. If you looked, you could see differences in the way they moved and spoke and used their hands. Over time, their personalities changed even the way that they looked. And of course Gemma was much heavier than Cassiopeia, and had long hair to her shoulders that looked soft to the touch. Gemma was nicer than Cassiopeia. More prone to worry, too. But they had the same stubbornness—that Lyra could see, too.

As soon as they were alone, Lyra went to the bookshelves. She could feel 72 watching her, but she didn’t care and couldn’t resist any longer. She reached up and ran a finger along the spines, each of them textured differently, some of them gloss-smooth and hard and others soft and crumbly like dirt. L-I-T-T-L-E W-O-M-E-N. Little Women. T-H-E G-O-L-D C-O-A-S-T. When she thought of The Little Prince, lost somewhere on the marshes, she still felt like crying. But these books made up for it, at least a little.

“You were telling the truth,” 72 said. He was watching her closely. “You can read.” He made it sound like a bad thing.

“I told you. Dr. O’Donnell taught me.” She kept skipping her fingers over the titles and, as she did, read out loud: “The Old Man and the Sea. The Long Walk. The Hunger Games.”

He came to stand next to her. Again she could smell him, an earthy sweetness that made her feel slightly dizzy. She’d never found out which of the males Pepper had been with, although Cassiopeia had said a male doctor, because of what happened at the Christmas party, because Pepper had been chosen. But she wondered, now, whether instead it was 72.

“Is it hard?” he asked.

“At the beginning,” she said. She didn’t know why she was thinking of Pepper. She took a step away from 72. “Not so much when you get the hang of it.”

“I thought only people could read,” he blurted out. When she turned to look at him, surprised by the tone of his voice, he turned away. “I’m going to get clean.”

A moment later, she heard the shower pipes shudder and the water start in the bathroom—a familiar sound that lulled her once again into exhaustion. She didn’t understand 72 and his rapid changes of mood. But he’d chosen to stay with her. He hadn’t left her behind. Maybe this complexity was a feature of the male replicas—she didn’t know, had never been allowed to interact with them.

She removed the file she’d taken from its filthy pillowcase and placed it carefully on the desk below the windows. Although she had a roomful of books now—a room full of books, an idea so exciting it made goose bumps on her arms again—the folder, and the single sheet of paper it contained, was her final tether to home. She recognized an old patient report—she’d seen enough of her own reports to recognize a version of the form still in use. But she was too tired to read, and she left the folder open on the desk and returned to the shelves, no longer trying to make sense of the words, just admiring the way the letters looked, the angles and curls and scrolled loops of them.

“I’m all done now.”

She hadn’t heard the shower go off or 72 emerge from the bathroom. She turned and froze. His skin, which had been streaked with blood and caked in a layer of sediment and crusted mud, was now as shiny and polished as a beach stone, and the color of new wood. His eyelashes, grayed by the ash, were long and black. A towel was wrapped around his waist. She was struck again by the strangeness of the male’s body, the broadness of his shoulders and the torqued narrowness of his muscled waist.

“Thank you,” she said, snatching up the clothes Gemma had left for her. She was careful not to pass too close to him when she moved into the bathroom. She shut the door firmly, a little confused by the mechanism of the lock. At Haven, all the doors locked with keypads or codes, except for the bathrooms, which had no locks at all.

She stripped down and balled her filthy clothes in a corner. She had never showered alone before and it felt wonderful: the big echoey bathroom, the space, the aloneness of it. Was this how all people lived? It felt luxurious to her. She spent a few minutes adjusting the taps, delighted by how quickly the water responded. In Haven, there was never enough hot water. The soap Gemma had bought was lilac-scented and pale purple, and Lyra found herself thinking of 72, naked, washing with purple soap, and the urge to giggle bubbled up in her chest, followed by a wave of dizziness. She had to sit with her head between her legs and the water driving down on her shoulders until it passed.

She lathered and rinsed her scalp, scrubbed her ears with a pinkie finger, washed the soles of her feet so that they became so slippery it was treacherous to stand. Finally she felt clean. Even the towels here were better than they were at Haven, where they were thin and stiff from hundreds of washings. Her new clothes felt soft and clean. Gemma had bought her cotton underwear in different colors. She’d never had underwear that was anything but a bleached, dingy beige. Looking at herself in the mirror, she almost could have passed for a real person, except for the length of her hair. She fingered the scar above her right eyebrow. She had scars all over her body now, from spinal taps and harvesting operations to test her blood marrow, but when she was dressed, most of them were concealed. Not this one, though.

In the bedroom, she found 72 stretched out on top of the covers, staring up at the ceiling fan. He was wearing new jeans that Gemma had bought for him, and this fact seemed only to emphasize his shirtlessness and the smooth muscled lines of his chest and shoulders. She’d never noticed how beautiful bodies could be. She’d thought of them only as parts, machine components that serviced a whole. She’d been interested in the males, of course—curious about them—but she’d also learned that curiosity led to disappointment, that it was better not to want, not to look, not to wonder. But she was suddenly terrified of lying next to him, although she couldn’t have said exactly why. Maybe because of what had happened to Pepper. But she thought it was more than that.

“What?” 72 sat up on his elbows. “Why are you looking at me like that?”

“There’s no reason.” Realizing she’d been staring, she forced herself to move to the bed. She slipped under the sheets—these, too, softer than any she’d ever known—and curled up with her knees to her chest, as far from 72 as possible. But still her heart was beating fast. She felt, or imagined she felt, warmth radiating off him. He smelled now a different kind of sweet, like shampoo and soap and fresh-scrubbed skin. For a long time they lay there together and she couldn’t stop seeing him next to her, couldn’t stop seeing his lashes lying on his cheeks when he closed his eyes and the high planes of his cheekbones and the darkness of his eyes.

He shifted in the bed. He put a hand on her waist. His hand was hot, burning hot.

“Lyra?” he whispered. His breath felt very close to her ear. She was terrified to move, terrified to turn and see how close he was.

“What?” she whispered back.

“I like your name,” he said. “I wanted to say your name.”

Then the bed shifted again, and she knew he’d rolled over to go to sleep. Finally, after a long time, the tension in her body relaxed, and she slept, too.

When she woke up, it was dark, and for a confused second she thought she was back at Haven. She could smell dinner cooking in the Stew Pot and hear the nurses move between the cots, talking to one another. Then she opened her eyes and remembered. Someone had shut the bedroom door, but a wedge of light showed from the living room. Jake and Gemma were talking in low voices, and something was cooking. The smell brought sudden tears to Lyra’s eyes. She was starving, hungrier than she’d been in weeks.

She eased out of bed, careful not to wake 72. She was vaguely disappointed to see they’d been sleeping with several feet of space between them. In her dream they had been entangled again, sweating and shivering in each other’s arms. In her dream he’d said her name again, but into her mouth, whispering it.

In the big room, Jake was bent over a computer laptop that sat next to a soda on the coffee table. He smiled briefly at Lyra. She was startled—it had been a long time since anyone had smiled at her, probably since Dr. O’Donnell—and she tried to smile back, but her cheeks felt sore and wouldn’t work properly. It didn’t matter. She was too late. He’d already turned his attention back to the computer.

Immediately, Gemma was moving away from the stove with a bowl, skirting the table that divided the kitchen from the library—Lyra thought it must be called a library, anyway, since Dr. O’Donnell had told her that libraries were places you could read books for free. “Here,” Gemma said. “Chili. From a can. Sorry,” she added, when Lyra stared, “I can’t cook.”

But Lyra had only been wondering at all her freedoms, at the fact that Gemma knew how to shop and get food and clothing. Wherever she’d been made, she must have lived for most of her life among real people.

“You need to eat,” Gemma said firmly, and seemed surprised—and pleased—when Lyra took the bowl and spoon and began to eat so quickly she burned the roof of her mouth. She didn’t even bother sitting down, both thrilled and disturbed by the fact that there was no one to yell at her or tell her to keep her seat.

“Transmissible spongiform encephalopathies,” Jake said out loud, still bending over his computer. “That’s a category of disease. Mad cow is a TSE.”

“Okay.” Gemma drew out the last syllable. “But what does that mean?” She went to sit next to Jake on the couch, and Lyra licked the bowl clean, after making sure neither of them was looking. Jake kept turning his soda can, adjusting it so that the small square napkin beneath it was parallel to the table’s edge.

“I don’t know.” Jake scrubbed his forehead with a hand and fixed his laptop so this, too, was parallel. “There are just references to it in the report.”

Lyra saw that next to Jake’s computer was the file she’d stolen from Haven. She set her bowl down on the table with a clatter. “You—you shouldn’t be looking at that,” she said.

“Why not?” Jake raised an eyebrow. “You stole it, didn’t you?”

“Yes,” Lyra said evenly. “But that’s different.”

“It’s not like they’ll miss it now. The whole place is an ash heap.”

In Lyra’s head, she saw all of Haven reduced to a column of smoke. Sometimes the bodies that burned came back to Haven in the form of smoke, in a sweet smell that tickled the back of the throat. The nurses hated it, but Lyra didn’t.

“Jake,” Gemma said.

He shrugged. “Sorry. But it’s true.”

He was right, obviously. She couldn’t possibly get in trouble now for stealing the file or allowing someone else to see it—at least, no more trouble than she was already in. Jake went back to thumping away at the computer. Gemma reached out and drew the file onto her lap. Lyra watched her puzzle over it, frowning. Maybe Gemma couldn’t read?

But after a minute, Gemma said, “Lyra, do you know what this means? It says the patient—the replica, I mean”—she looked up as though for approval, and Lyra nodded—“was in the yellow cluster.”

The yellow cluster. The saddest cluster of all. Lyra remembered all those tiny corpses with their miniature yellow bracelets, all of them laid out for garbage collection. The nurses had come through wearing gloves and masks that made them look like insects, double wrapping the bodies, disposing of them.

“The Yellows died,” she said, and Gemma flinched. “There were about a hundred of them, all from the younger crops. Crops,” she went on, when Gemma still looked confused, “separate the different generations. But colors are for clusters. So I’m third crop, green cluster.” She held up her bracelet, where everything was printed neatly. Gen-3, TG-GR. Generation 3, Testing Group Green. She didn’t understand why Gemma looked sick to her stomach. “They must have made a mistake with the Yellows. Sometimes they did that. Made mistakes. The Pinks died, too.”

“They all died?” Jake asked.

Lyra nodded. “They got sick.”

“Oh my God.” Gemma brought a hand to her mouth. She seemed sad, which Lyra didn’t understand. Gemma didn’t know anyone in the yellow cluster. And they were just replicas. “It says here she was only fourteen months.”

Lyra almost pointed out that the youngest had died when she was only three or four months, but didn’t.

“You said colors are for clusters,” Jake said slowly. “But clusters of what?”

Lyra shrugged. “There are different clusters, and we all get different variants.”

“Variants of what?” he pressed.

Lyra didn’t know, exactly, but she wasn’t going to admit it. “Medicine,” she said firmly, hoping he wouldn’t ask her anything more.

Gemma sucked in a deep breath. “Look, Jake. It’s signed by Dr. Saperstein, just like you said.”

“Dr. Saperstein is in charge of the growth of new crops of replicas,” Lyra said. Despite the fact that she was still annoyed at Jake and Gemma for looking at the file—the private file, her file—she moved closer to the couch, curious to know what they were doing. “He signs all the death certificates.” Beneath his was a second signature, a name she knew well. Nurse Em had been one of the nicer ones: Nurse Em had taken care when inserting the needles, to make sure it wouldn’t hurt; she had sometimes told jokes. “Nurse Em signed, too.”

“Nurse Em.” Gemma closed her eyes and leaned back.

“Holy shit,” Jake said, and Gemma opened her eyes again, giving Jake a look Lyra couldn’t decipher.

“Nurse Em was one of the nicest ones. But she left,” Lyra said. An old memory surfaced. She was alone in a hallway, watching Dr. O’Donnell and Nurse Em through a narrow crack in a door. Dr. O’Donnell had her hands on Nurse Em’s shoulders and Nurse Em was crying. “Think of what’s right, Emily,” Dr. O’Donnell said. “You’re a good person. You were just in over your head.” But then Nurse Em had wrenched away from her, knocking over a mop, and Lyra had backed quickly away from the door before Nurse Em barreled through it.

But that couldn’t have been a real memory—she remembered a janitor’s closet but that couldn’t be right, not when the nurses and doctors had break rooms. And Nurse Em had been crying—but why would Dr. O’Donnell have made Nurse Em cry?

“Let me see that.” Jake took the file from Gemma and leaned over the computer again. Lyra liked watching the impression of his fingers on the keys, the way a stream of letters appeared as though by magic on the screen, far too fast for her to read. Click. Click. Click. The screen was now full of tiny type, photographs, diagrams. It was dizzying. She couldn’t even tell one letter from another. “This report—all of this terminology, TSEs and neural decay and protein folding—it’s all about prions.”

“Prions?” Gemma said. She’d clearly never heard the word before, and Lyra was glad that for once she wasn’t the one who was confused.

“Bacteria, viruses, fungi, and prions,” Jake said, squinting at the screen. “Prions are infectious particles. They’re proteins, basically, except they’re folded all wrong.”

“Replicas are full of prions,” Lyra said, proud of herself for knowing this. The doctors had never said so directly, but she had paid attention: at Haven, there was very little to do but listen. That was the purpose of the spinal taps and all the harvesting—to remove tissue samples to test for prion penetration. Often when replicas died they were dissected, their bones drilled open, for the same reason. She knew that prions were incredibly important—Dr. Saperstein was always talking about engineering prions to be better and faster-acting—but she didn’t know what they were, exactly.

Jake gave her a funny look, as if he had swallowed a bad-tasting medicine.

“I still don’t get it,” Gemma said. “What do prions do?”

He read out loud: “‘Prion infectivity is present at high levels in brain or other central nervous system tissues, and at slightly lower levels in the spleen, lymph nodes, bone marrow. . . .’ Wait. That’s not it. ‘If a prion enters a healthy organism, it induces existing, properly folded proteins to convert into the disease-associated, misfolded prion form. In that sense, they are like cloning devices.’” He looked up at Gemma, and then looked quickly down again. “‘The prion acts as a template to guide the misfolding of more proteins into prion form, leading to an exponential increase of prions in the central nervous system and subsequent symptoms of prion disease. This can take months or even years.’” He put a hand through his hair again and Lyra watched it fall, wondering whether 72’s hair would grow out now, whether it would fall just the same way. “‘Prion disease is spread when a person or animal ingests infected tissue, as in the case of bovine SE, or mad cow disease. Prions may also contaminate the water supply, given the presence of blood or other secretions. . . .’”

“So prions are a kind of disease?” Gemma asked.

“The bad kind of prions are disease,” Jake said quietly.

“That can’t be right,” Lyra said. She was having trouble following everything that Jake was saying, but she knew that there, at least, he was wrong. She knew that replicas were physically inferior to normal humans—the cloning process was still imperfect, and they were vulnerable. That was the word the doctors and nurses always used when they lined up vitamins and pills, sometimes a dozen in a row. But she’d always thought—and she didn’t know why she’d thought this, but she knew it had to do with things overheard, sensed, and implied—that prions were good. She’d always had the impression that this was a single way in which replicas were superior to humans: their tissue was humming with prions that could be extracted from them.

She felt a curious tickle at the back of her throat, almost as if she had to sneeze. Sweat prickled in her armpits.

Jake wouldn’t look at her. She was used to that.

“Listen to this.” Jake had pulled up new writing—so many lines of text Lyra felt vaguely suffocated. How many words could there possibly be? “Google Saperstein and prions and an article comes up from back in the early 1990s. Saperstein was speaking at a conference about biological terrorism. ‘Chemical weapons and viral and bacterial agents are problematic. Our soldiers risk exposure even as the weapons are deployed against our enemies. War is changing. Our enemies are changing, growing radicalized and more diverse. I believe the future of biological warfare lies in the isolation of a faster-acting prion that can be distributed via food supply chains.’” Jake was sweating. And Lyra had been sweating too, but now she was cold all over. It felt like she had to use the bathroom, but she couldn’t move. “‘We might cripple terrorist groups by disseminating doctored medications and vaccinations, which will be unknowingly spread by health care workers in dangerous and remote environments immune to normal modes of attack.

“‘All known prion diseases in mammals affect the structure of the brain or other neural tissue and all are currently untreatable and universally fatal. Imagine’”— Jake was barely whispering—“‘terrorist cells or enemy insurgents unable to think, walk, or speak. Paralyzed or exterminated.’”

“Oh my God,” Gemma said. She brought a hand to her lips. “That’s awful.”

From nowhere a vision came to Lyra of a vast, dust-filled field, and thousands of bodies wrapped in dark paper like the Yellows had been, still and silent under a pale-blue sky.

What was it that Jake had read?

All known prion diseases in mammals . . . are currently untreatable and universally fatal.

“Jesus.” Jake leaned back and closed his eyes. For a long time, no one said anything. Lyra felt strangely as if she had left her body behind, as if she no longer existed at all. She was a wall. She was the floor and the ceiling. “That’s the answer to what they were doing at Haven.” Although he’d addressed Gemma, when he opened his eyes again, he looked directly at Lyra, and immediately she slammed back into her body and hated him for it. “Prions live in human tissue. Don’t you see?”

Lyra could see. But she couldn’t say so. Her voice had dried up. She was filled with misfolded crystals, like tiny slivers of glass, slowly cutting her open from the inside. It was Gemma who spoke.

“They’ve been experimenting on the replicas,” she said slowly. She wouldn’t look at Lyra. “They’ve been observing the effects of the disease.”

“Not just experimenting on them,” Jake said, and his voice broke. “Incubating them. Gemma, they’ve been using the replicas to make prions. They’ve been growing the disease inside them.”

Turn the page to continue reading Lyra’s story. to read Chapter 10 of Gemma’s story.