So, a preface. This is a sequel to "Just a Few Broken," but it has a fairly different tone and intended audience. Most notably, there's a substantial subplot here that explores the Indoctrination Theory. I'm going to do my best to make the first story optional reading, as I feel this story is shaping up to be significantly better.

If you're new, below is a lengthy summary (sorry) of the events of the previous story. Otherwise, feel free to jump to the next chapter.

Dr. Kaya Cole, a twenty-five year old recent medical school graduate, was working undercover for a joint military-CIA operation, seeking to infiltrate one of the early Martian colonies sixty years before the start of Mass Effect. They suspected human trafficking and possibly unethical human experiments were occurring. Kaya is also a psychic. She was exposed to a synthetic eezo-like compound when she was twelve, following an industrial accident in Okinawa rather similar to what happened in Bhopal in its scope and devastation.

The incident killed her father with a slowly metastasizing but persistent lung cancer over the next two years, and Kaya realized her abilities shortly after his death. She moved back with her mother – Dr. Cassandra Cole – in Washington, DC. However, the events in Okinawa took a heavy toll on Kaya's psyche, which was made even worse by her sudden emergence of psychic abilities.

At fifteen, Kaya attempted suicide during a manic episode. She was sent to St. Vincent's school in London, an international school with a reputation for excellent academics as well as top-notch psychiatric care. However, the school – as a common place for children from both military and rough backgrounds with exceptional intelligence – was also a recruiting point for several major intelligence agencies. Kaya's abilities were identified by a CIA recruiter named Cain, who brought her into the program and began training her as a teenager.

Kaya's first real field mission was to be the mission at the Martian colony, Drake's Point, ten years later. At the time, the trip took about six months, and colonists were put into cryostasis to save resources. Someone from one of the corporations in charge of Drake's Point is believed to have identified Kaya as an agent, causing them to sabotage the colonists's ship, the Magellan.

It's Captain Shepard and her crew – Garrus, Kaidan, James, and Liara – that find Kaya seventy years later, five years after the events of ME3. She is the only survivor of the Magellan's destruction, and her life pod remained powered and intact. Miranda uses her talents to help Kaya recover in a hospital on the Citadel, given that the technology aboard the Magellan was never intended to sustain cryostasis for so long. Then, after the Normandy has departed for a new mission, Kaya is kidnapped by a scientist formerly of Project Indigo. Indigo was the project code name for Kaya's small team seventy years ago.

It turns out, as Jack explains when the team returns to the Citadel, that Indigo is still alive. A handful of people – thirteen in fact – were identified after the discovery of eezo to have developed talents similar to Kaya's. Jack herself is working on the project with kids at Grissom Academy. The scientist who kidnapped Kaya, Dr. Marcus, has very different ideas about where Indigo should go.

The team rescues Kaya in Omega, where they find that Marcus has been torturing Kaya in an attempt to reveal abilities that amount to an extreme, rapid form of indoctrination. It turns out that he succeeded, as Kaya forces Marcus to shoot himself in the head after Shepard's team arrives. She repeats this horror a few days later, when the Normandy is attacked by a Cerberus crew with intimate knowledge of her cyberwarfare and stealth capabilities. As Cerberus troops are boarding, Kaya enters the mind of a Cerberus soldier and forces them to turn off both life support and their cyberwarfare suite inside the Cerberus ship. The Normandy gets away, although three Alliance soldiers are killed.

Hackett – who is none too fond of Kaya's insubordinate tendencies – informs Shepard and Kaidan that Dr. Marcus appears to have followers within the Alliance. He instructs them to run, hiding Kaya aboard the Normandy, following the events with Cerberus. While Hackett plants intel suggesting that Kaya has gone rogue while the Normandy was docked in Vancouver, the crew continues on their normal missions.

During this time, a romance develops between Joker and Kaya. However, it also becomes apparent that Kaya is extremely emotionally unstable. Marcus's interference – including implanting her with a modified biotic amp – have significantly changed her powers. While she gains biotic abilities, she also gains the ability to relive the memories of various people aboard the Normandy, and her mind tends to gravitate toward the particularly bad ones.

After following some intel on Kaya to Rannoch, where they pick up Tali, the crew heads to Palaven to help with a Krogan-Turian peace meeting. It's shortly after this embarkation that Kasumi slips aboard the ship, revealing that she is Kaya's grand-niece and providing intel for their next step on the journey. While on Palaven, Kaya also has a seizure induced by a post-traumatic episode and a malfunctioning biotic amp. Following the seizure, she wakes up and convinces Jeff to get a drink with her on Palaven, even though she is supposed to be confined to the ship.

Her immature display greatly pisses off the crew, especially Shepard. However, there's not much time to dwell on it, as the crew soon follows Kasumi's lead on Cerberus to London and rescues Miranda from a cell that had captured and tortured her. They follow Miranda's intel to an office in London, where Maya Brooks, recently escaped from prison, attempts to ambush them.

Brooks is brought back to C-Sec for interrogation. She reveals that Binary Helix is behind the Indigo cell Marcus was working with, and that there are still unfriendly elements within the Alliance. When Kaya confirms that Brooks is actually telling the truth, Shepard states that she "doesn't make the same mistake twice" and shoots Brooks in the head.

Shepard, Kaidan, and Garrus then proceed to make a deal with both the Alliance and the Council. Shepard will retire from the Normandy, turning it over to Kaidan, who will lead the vessel under both Alliance and Council authority. Kaidan will have sole jurisdiction over Kaya – who both the Alliance and the Council want badly for her power – in an attempt to keep her out of any unsavory hands while keeping a diplomatic peace. Eventually, both sides agree to his terms, including Kaya's honorable discharge from the military.

The story ends with Joker and Kaya in the XO's cabin aboard the Normandy. Joker is still upset with the Spectres for brokering a deal that places Kaya in the line of fire, particularly given her extremely fragile mental state. However, Kaya finds herself looking forward to new adventures, and reflects that she has gained more than she's lost in the overall experience.