-Galen and Lyra are researching synthetic kyber crystals in the first year of the Clone Wars on the planet Vallt when a pro-separatist faction overthrows the government and imprisons them, trying to get them to aid the CIS. Galen refuses, and as a pacifist he won't help the Republic either.
-After the Second Battle of Geonosis, the Republic "somehow" comes into possession of the Death Star plans (obviously Palpatine's doing) and believes that the CIS is building a superweapon. The Special Weapons Group is tasked with reverse engineering the schematics and building it first, and Lt. Commander Orson Krennic - who was in the Futures Program with Galen - convinces Mas Amedda to rescue the Ersos, believing Galen's genius is crucial to making scientific breakthroughs for the necessary power.
-Krennic pretends to be an employee of Galen's company, Zerpen, and makes a prisoner swap with the separatists for Galen, providing two separatist scientists he had kidnapped, and after the escape the Republic bombards the separatists on Vallt. Krennic takes Galen to his homeworld, Grange, and makes him witness the CIS siege there to try to sway him to join the Republic but Galen refuses.
-The Ersos are kept under watch on Coruscant as the military tries to determine if they are a security threat as possible double agents. Galen is eventually exonerated on Krennic's word but he has trouble finding a job since everything in his field is tied to the war effort. Some other colleagues see him as a traitor. Months pass and Krennic preys on his insolvency getting him a job on Lokori for Helical HyperCom as a QA tech which he hopes will bore him to death and make him strive for more.
-Meanwhile, Krennic slyly convinces Poggle the Lesser, who is in captivity, to help the Republic, since Geonosians by nature need to build and become violent without work. Poggle is reinstated as a Republic vassal and announces to the Geonosian public that the Geonosians will construct their grandest project yet. They are tasked with working on the Death Star which is taking shape in orbit, the most basic ring having been built already by droids. However, Poggle purposefully overstaffs the project, making the drone workers restless, leading to them revolting and sabotaging months of work. In the chaos, Poggle escapes (which ties up a plot hole from TCW since it never explained how he escaped before RotS).
-Lokori comes under CIS assault until the end of the war. The Ersos almost die but are saved when the droid armies are shut down. They relocate back to Coruscant where Krennic proposes a new job as the head of Project Celestial Power, a postwar reconstruction project that he pitches as "the Emperor's dream" since it will focus on supplying cheap power to worlds damaged by the war. Galen jumps at the chance when he learns he will be working with kyber crystals since the Jedi can no longer hoard then, but Lyra is somewhat offended because she doesn't think they should tamper with the Force.
-Galen becomes enamored with his work and Krennic secretly has his notes supplied to a sister site on Malpaz where other scientists can study how to apply his research to weaponization of kyber crystals. However, they accidentally blow up the facility.
-Krennic becomes aware that Tarkin is his rival for the Emperor's interest as his constant setbacks and failure to convince Galen to participate in the program have turned Amedda against him. With the Geonosis asteroid belt mined dry, he convinces Tarkin to sign off on a plot to obtain resources from untouched "Legacy" planets which act as nature preserves by planting weapons caches there and claiming that separatist holdouts use them, giving the military pretext to take control of the planets and then mine them.
-Fearing that Lyra is too indepdendent, Krennic gets her a job on a scouting expedition on Alpinn to research a possible kyber vein, which keeps her and young Jyn out of the picture for months. He shows Galen the destroyed facility on Malpaz and claims that neoseparatist anarchists destroyed it and that their movement is spreading, hoping to convince Galen that his and Palpatine's dream will never be realized if he does not work with the military.
-After the expedition on Alpinn, Has Obitt (a smuggler Krennic had been using throughout the book to do his dirty work, like kidnap those scientists, drop the weapons on Legacy worlds, and fly Lyra out to Alpinn) has a crisis of conscience and shows Lyra the ruined Legacy worlds. Lyra comes to understand that Krennic is up to something. She gets extra freaked out when Krennic starts spying on her, following her to a playground on Coruscant where Jyn is playing to tell her not to cause stress for Galen.
-Galen drifts away from Lyra, obsessed with his work and thinking that she is wrong about Krennic, making excuses about the Empire making hard choices for the greater good when she tells him about the Legacy worlds. But he starts to get suspicious and looks into secret files on the other scientists and projects, revealing that the material from the Legacy worlds is not being accounted for. He starts to put two and two together and realizes his work is being weaponized.
-After finding out about Has' betrayal, Krennic sets up an elaborate scheme where he hires Has for what he promises to be a last mission to drop cargo in the Salient system to allow the Empire pretext to take it over to hunt for separatists; Tarkin is partially in on it but doesn't realize that Krennic knows that Has will break. When the inhabitants of Salient refuse to allow the Empire to take control, Has gets tangled up in a resistance movement with Saw Gerrera, which bogs down Tarkin for months as his understaffed group is forced to fight an insurgency. Tarkin realizes that Krennic set him up and after capturing Has he decides to use him as his own spy.
-Krennic has a bunch of scientists successfully create an early version of the superlaser using Galen's notes, which they fire on twin black holes. Afterwards he has the scientists, who were based on Hypori (including the Ersos' friend Reeva) disappeared and wiped from the Imperial archives, probably to work on Geonosis.
-The Ersos find out that Reeva and the others have gone missing. Galen finally admits to Lyra that he was wrong and that they have to escape. They sneak out during a holiday celebration, making it difficult for Krennic to follow them due to the crowds. Tarkin sends Has to Coruscant to mess with Krennic, unaware of the situation with the Ersos, but Krennic thinks that Has has come to pick them up. Has uses the confusion to his advatage, telling Krennic he's just meeting with another smuggler, and when they check his records he's right. Meanwhile, the Ersos meet up with Saw Gerrara who takes them to the planet Lahmu where they go into hiding.
-Krennic and Tarkin both hire Has, with Tarkin having Has spy on Krennic while Krennic has Has try to hunt down the Ersos. Obviously Has makes this difficult so that nothing gets accomplished.
-Tarkin is put in charge of the Death Star project due to his successful conquest of Salient and Krennic gets bumped down because of his loss of Galen.