The Big Synopsis
Spoilers through "Her Hardest Hue To Hold"
Leo Amara was dead, to begin with.
The U.S.S. Excelsior's chief of special operations keeled over during the ship's last mission, one of dozens of victims of a virulent disease known as "The Wasting." The Wasting was cured, but Amara was too far gone to survive.
Or was he? When Doctor Melissa Sharp's autopsy revealed ten cc's of warp plasma in his blood, Amara's death was ruled a homicide. The surly Lt. Asuka Yubari, "on loan" to the Excelsior from Starfleet Intelligence (Special Projects Division), agreeed to investigate. Unfortunately, the killing didn't stop there; just a few hours later, Lt. David Robins, an engineer from the U.S.S. Sizemore (assisting with the Excelsior's repairs) was killed when a bulkhead he working on exploded. That, too, was ruled a homicide.
Yubari couldn't get very far before she was kidnapped by her own boss, General Isaac Brahms of Special Projects, who took the drastic step of secretly detaining her aboard his ship, the Renegade, for the mere "crime" of having blown her cover to the Excelsior crew. Startled but capable, Yubari soon escaped, taking Brahms into custody on her way back to the Excelsior.
But answers have begun to form. Just before he died, Leo Amara gave Lt. Alex Rol a computer chip. Rol read and erased the chip, and would have gotten away with it had not Chief Engineer Alecz Lorhrok confronted Rol in his quarters, looking for the chip. Rather than allow Lorhrok to restore and read the chip, Rol vaporized it with a phaser -- apparently under some kind of compulsion to do so. Lorhrok disabled Rol, and, when Rol revived, the captured man explained that he was an unwilling agent of Special Projects; that he was being "genetically controlled" by nanites in his bloodstream; and that, under orders from Brahms, he had personally killed both Amara and Robins under the influence of this supposed "genetic control." Lorhrok seemed convinced by the evidence Rol provided, including scans of the nanites, but had Rol thrown in the brig for good measure until the captain could make a decision.
Meanwhile, Captain Rachel Cortez, in a coma ever since sustaining injuries in bladed combat on Valandria, briefly regained consciousness. She was able to relate a few cryptic clues to her first officer, Commander Alcar Dovan, including a set of coordinates and a warning that "Brahms is wrong" before she died peacefully of heart failure. Commander Dovan reluctantly took command of the Excelsior.
As we enter the penultimate act of our little drama, all roads seem to lead to Brahms. But who is Isaac Brahms? Why does he do what he does? How can he be stopped?
And whose side is Alex Rol really on?