The fic centers on Alexander Wallace, a subject of the Jaeger Program, an attempt by Dr. Polendina to create a hundred of the greatest Huntsman on Remnant. Sadly, things go bad when he's replaced by Commander Vasilyevich, who devotes their efforts into killing Faunus and Faunus sympathizers. Alexander proves to be the sole survivor of the program, and personally kills Vasilyevich before being rescued by General Ironwood.
From there, the fic chronicles Alexander's life as he attends Beacon Academy, rejoins the Atlesian Military, and eventually gets involved in the fight against Salem.
AQUA: The First Step contains examples of the following tropes:
- Bully Hunter: At one point, Amber comes across a group of people bullying a dog Faunus and beats the ever-loving crap out of them.
- The Dog Bites Back: After enduring Vasilyevich's cruelty for over a year, Alexander ultimately rallies the remaining kids in the Jaeger Program to fight back against him; he proves to be the only survivor, and personally kills Vasilyevich before broadcasting the outside world for help.
- Fatherly Scientist: Dr. Polendina was beloved by all of the children in the Jaeger Program, visiting them once a week and teaching them social skills.
- General Ripper: Vasilyevich is noted by Dr. Polendina to be one of the worst commanders the Atlesian army has ever seen, known to unnecessarily sacrifice his own men to ensure a victory. Under his lead, the Jaeger Program is perverted and set up as an anti-Faunus assassin group, and all but Alexander are either killed after attempting to escape or commit suicide.
- Like Brother and Sister: Alexander ends up partners with Amber during their Beacon Academy days, and eventually develop this kind of relationship. Amber even remarks at one point that she's Alexander's sister "in all but blood."
- The Mole: Blake ends up becoming one to Alexander for the White Fang as part of an immunity deal. When she eventually decides to leave, Alexander pulls some strings to get her into Beacon.
- Screw the Rules, I Have Connections!: According to Dr. Polendina, the only reason Commander Vasilyevich still had a job in the army despite his General Ripper tendencies is because Jacques Schnee backed him up, bribing people and pulling strings to keep him employed.
- Sherlock Scan: Alexander is able to quickly deduce that General Ironwood is a cyborg due to his Conspicuous Gloves, the smell of hydraulic fluid, and the sound of gears when he moves.
- Tyrant Takes the Helm: Dr. Polendina, a Fatherly Scientist, is initially the director of the Jaeger Program. But after one of the girls sees the horrors at a drug kingpin's house and commits suicide, unable to cope, he's replaced with Commander Vasilyevich, a General Ripper who devotes his time and effort to having them kill Faunus and Faunus sympathizers. Eventually, Alexander and the remaining kids rebel and kill him.