The Andromeda Evolution

50 years after the first Andromeda incident, an anomaly is found deep in the Amazon rainforest. A large, black structure has appeared, killing off every lifeform in its path. “Project Eternal Vigilance”, a project dedicated to keeping an eye out for the Strain, suspects it to be a mutant version of Andromeda. The anomaly is reported and another “Project Wildfire” takes off.

Nidhi Vedala, Harold Odhiambo, Peng Wu, Zachary Gordon, and Sophie Kline are selected as the field scientists for the investigation by computer generation. However, overseer General Stone replaces Gordon with James Stone, the son of Jeremy Stone, based on a hunch.

The field scientists are told about their positions and ushered to a spot in the rainforest right outside of the quarantine zone for the anomaly. Sophie Kline does not appear, noting that she is an American astronaut residing at the International Space Station, who also suffers from ALS. Stone arrives late because he was added at the last minute, sparking tension between him and the leader, Vedala (who also does not believe he is qualified to be there).

The group starts off towards the anomaly (despite Kline's constant disapproval), led by Sergeant Eduardo Brink and guided through the rainforest by natives. As Kline studies the anomaly from space, she confirms that it is a new strain of Andromeda: AS-3. After seeing many ominous signs from the native tribes, the group decides to stop for the night. In the darkness, a tribe attacks in a strangely violent manner. All of the guides are taken down and Brink kills off all of the tribe members. However, he is struck in the shoulder with an axe contaminated with the AS-3, and dies overnight. Peng finds an Omega poison in his bag, and keeps it. She does not feel as if she can trust the others with her new knowledge due to a pre-existing anxiety disorder.

The field scientists are alone, and begin studying the tribe members’ bodies. They figure out that they were infected with the AS-3, and had been mining the anomaly to create weapons (such as Brink's fatal arrow). Meanwhile, Odhiambo points out a little tribal boy who had been hiding. The kid does not appear to be sick. Stone uses a translation device to converse with the boy, who reveals that his name is Tupa. Tupa explains that he is the only surviving member of his tribe. He and James Stone become inseparable, much to Vedala's discomfort.

Meanwhile, the team misses their rendezvous with Stern due to the circumstances. The government is planning to resort to “Operation Zulu” to get rid of the anomaly, a plan which would wipe out the scientists as well. With this knowledge, Kline tries to reach Brink, not knowing of his death. She asks him to use the Omega, and Peng, knowing what that means, informs the others that for some reason Kline wants them dead. They set up a sign saying “ALIVE” to reveal that they are not dead yet, and continue on.

Once they get to the anomaly, the group realizes that it is constantly growing, and that it is extremely hot. Peng becomes increasingly anxious. They decide to enter the anomaly through its opening, much to her discomfort. Stone orders Tupa to stay back, but the boy secretly follows soon afterwards. Inside the anomaly, Stone uses drones to check ahead. They find the mangled body of a white man melted into the floor inside, raising questions as to where they are. They then come to the realization that they are in a capsule building. They enter a room to find many other bodies - construction workers, and the source of the Andromeda anomaly.

As they look around, they find a control hatch leading down under the Amazonian lake it had landed over. As they continue to explore and discover, a radio transmitter is stimulated and Sophie Kline's voice comes over the radio. She explains that they have reached the control room, and that she warned them to stay away. Tupa is revealed and runs to Stone as Peng verges on a panic attack. Then, a broken propeller starts again and the Andromeda reactivates. As the floor becomes quicksand, they rush under to the hatch they found previously. Vedala ushers Peng along, but she is preparing to make a run for a different exit instead. Vedala watches as she runs and trips, and begins dying of infection. As she lies on her back in agony, she reveals to one of Stone's drones in her dying breaths that the Andromeda is on every planetary body in the solar system. It was alien machinery, looking for other life forms.

Meanwhile, Kline locks up her fellow astronauts and begins working against the Andromeda, a long-awaited plan. She sees it as yet another threat, and she creates a “space elevator” from the anomaly and tries to create a new strain based on AS-1 and AS-2 to defeat AS-3 with the help of her robot, despite Stern's begging for her to stop. She built the anomaly.

As the remaining team in the Amazon continue down the hatch, water from the river starts coming. The team rushes to escape it and to find a way out. Stone tries to help Odhiambo, who is older, but eventually it becomes worthless. Odhiambo begs for Stone to save himself, so Stone leaves him behind as Odhiambo drowns to death Eventually out of the hatch, Stone is left with just Vedala and Tupa.

They realize that Kline has created a space elevator. Communicating with Stern, Vedala notes that the only way that they can stop Kline is to do so directly: traveling to the ISS. Her and Stone go up to the ISS through the space elevator, and are forced to face Kline.

They find her dying of her own creation. They beg for her to stop, yet Kline resists and upsets Stone by calling him, “Jamie.” Eventually, she brings out her robot to fight them directly. It being much more powerful than either scientist, they are completely powerless to it. It breaks in Stone's helmet, and he realizes that the only way to stop it is to stop Kline herself. So, he uses the Omega poison against her, stored in his pocket to keep away from Tupa. Kline is killed, along with her robot.

Vedala, who now has major injuries from the robot's attack, approaches Stone and realizes that he has gotten infected from breathing in the strain. He tells her to leave him to die, yet as she goes she tries to think of ways that he can live. They start admitting things to each other, and he eventually admits that Jeremy Stone adopted him, and that he was “Jamie Ritter”, the baby from the first incident. Vedala realizes that Stone has benign microparticles still in his lungs from his first infection, protecting him and making him immune from Andromeda. The two continue onwards.

The other two astronauts put Vedala on morphine, yet someone still needs to sever Kline's ribbon to finally stop her plan. James Stone goes back down through orbit to do so, and as he is forced to speed up due to Kline's creation's acceleration, he briefly sees his dead mother from Piedmont who assures him that he needs to stay alive. He continues and gets the deed done, eventually reuniting with Tupa who had found his way out of the anomaly. The two were both the sole survivors of their respective birthplaces. Afterwards, Stone and Vedala are hinted at getting married and adopting Tupa. At the very end, Stern and a group of other scientists notice that Andromeda has reached Saturn and is directly connecting to an unknown extraterrestrial source.

General R. Stern: A four-star US general in command of NORAD (Colorado), leader of the Amazon mission.

Dr. James Stone: The adopted son of Dr. Jeremy Stone, robotics and artificial intelligence expert. (also a Piedmont, Arizona AS-1 survivor)

Dr. Nidhi Vedala: A nanotechnology expert who developed a spray to prevent infection by Andromeda AS-3 particles.

Dr. Sophie Kline: An ISS astronaut and expert in robotics and nanotechnology, who suffers from ALS.

Peng Wu: A soldier, doctor, pathologist and former taikonaut who suffers from an anxiety/panic disorder.

Harold Odhiambo: A scientist well-studied in anthropology, biology, and geology.

Tupa: A 10-year-old boy, the sole survivor of an Amazon tribe wiped out by the AS-3.

Crichton's widow, Sherri, recruited Wilson to write the sequel.[2]