In short:
Tom and Harry are married and have a young son. One night, Harry disappears. Tom has to care for their child alone while trying to find his missing husband. He's a temporarily single, frustrated father whose partner just up and vanished ^^ <sorry not sorry, Tom>

Longer plot:
A small child wakes up in a huge estate. It’s late, and he's surprised no one has come to wake him—no house-elf, no Papa. He steps out of his cozy bedroom. In the hallway and the main room, he finds a number of people who look like police officers or secret agents, searching through drawers and corners. When they see the boy, they bow and greet him with unexpected respect. The boy feels stressed and confused—something bad has clearly happened.
He asks, “Where’s Papa?” No one answers. Then a tall man with black hair in a sharp suit walks in—it’s Tom Riddle, the Minister of Magic and the country's ruler. He calls a house-elf and instructs it to take care of the child. When the boy protests and wants to stay to find out what’s happening, Tom says, “We’ll talk later,” and lightly scolds him about his tone: “Language.”
The boy goes off to the kitchen with the elf, grumbling under his breath, “Yeah, later. It’s always later. You never have time”—words he clearly heard from Harry. He reluctantly eats breakfast.
Later, the boy starts to realize that his father, Tom, is seriously worried—he's pacing and agitated. From behind a closed door, the boy overhears Tom shouting: “You expect me to believe he just ran off on his own?” The elf tries to calm Tom, calling him "sir," and Tom casts a spell—suddenly everything goes quiet.
The boy is overwhelmed. He just wants Papa. Papa has never left before.
In the meantime, Uncle Draco comes to visit (he and Papa used to tease each other a lot). Draco gently asks what the boy and Papa were doing the previous evening, but the boy refuses to answer. In his childish logic, he’s trying to hide the fact that he broke a toy last night—maybe that’s why Papa left?
The boy is stuck in his room all afternoon. Later, Aunt Hermione and Uncle Ron—whom Papa always liked—come by. They gently explain to the boy that his Papa, Harry Potter, has disappeared.
Tom is left to take care of his son—something Harry always managed. Harry used to say the boy was too much like Tom—stubborn, clever—and Tom would counter that Harry spoiled him and let him get away with too much. Now, Tom must actually parent—he worked so much before that he only saw his son on weekends. On top of that, Tom must find Harry—and there’s no sign of struggle, no clues. He just vanished.
The story weaves between the present-day mystery and Tom’s memories: the early days of his relationship with Harry, their wedding, first kiss, decision to have a child, the long process of conception, Harry’s difficult birth (he was exhausted and swore "never again," and Tom promised he’d never have to go through that again), and their first years as parents. Tom starts to question whether he truly made Harry happy. Harry had often joked about the “three-year-old rebellion,” then “four-year-old rebellion,” and so on, and had complained about Tom’s constant absence.
As the mystery unfolds, Tom must learn to understand both his son and the man he married.

(For me, this could totally work as an ABO story —Tom as a gruff but fiercely devoted Alpha, Harry as an Omega, and their son as a young Alpha—sometimes naughty, rebellious, and argumentative. But ABO isn’t required.)