Something was wrong with James. Harry knew that. Ginny said that the boy was fine, no different than normal, and that Harry was just being paranoid. He was working too hard, she said. He was stressed all the time. But Harry knew something was off about his son. It was in the way he smiled only when he was told to, or when something was in pain. It was in the way he never said "I love you" in a way that seemed like he meant it. There was something off about James Sirius Potter, but Harry didn't know what.
He started to suspect when it became clear there was also something wrong with Albus. It was worse with him. Harry caught him summoning and killing mice in the shed. He was a bully in his muggle primary school, although Ginny refused to admit it. They fought bitterly over it, worse still when Harry said they shouldn't have a third child because it was clear they weren't fit to be parents. But Lily came, and she was normal, and Harry and Ginny made up, and James understood that his antisocial behavior was scaring his dad and started to try to make real friends. But there was still something wrong with Albus.
James went to Hogwarts. He was sorted into Gryffindor. Nearly immediately Minerva wrote home that he was not fitting in with the other boys. He couldn't relate to them, he said. They were silly. Ginny raged about it, but Harry demanded that his eldest son submit to a mind healer. The result came back and shook Harry to the core. His son was a sociopath. The only reason he was as well adjusted as he was was because Harry had put in the effort to teach him to be kind, and James had been willing to listen. With therapy, James could fit in well enough, but he would always be different. Harry thanked Magic for this answer and this hope, but that night his eyes rested on his second son just a bit longer. His second son had always shut him out.
Harry had never liked healers. In his youth, the Dursleys had never taken him to a doctor. At Hogwarts, Madame Pomfrey had been brisk with him, especially because he was always in there. Now, as an Auror, he had mandatory physicals every six months. He always fought with Ginny more in the two weeks leading up to them. Now he sat in the waiting room, watching every healer rush past while the press sulked by the door. Albus was in the room in front of him, injured in a duel in the corridor well after curfew. His opponent was in another room down the hall. Both boys were in deep trouble, both physically and at school. They would be lucky if they were only suspended.
Harry had already spoken with the professors and the press. It was abundantly clear that Al was at fault for starting this mess, and as such Harry would stand by any and all punishment the school cast down upon him. If Al was expelled, well… they would cross that bridge when they came to it. Harry was also paying for the care of the other boy. When Al awoke, they would have a nice long conversation about how he would take care of that. Ginny didn't know about that fact yet. As a matter of fact, she wasn't even aware Al was in St. Mungo's. She was off playing an away quidditch game. Harry was supposed to be there, and would definitely hear about it later, but at the moment, Al was more important.
Finally, the door opened and a healer approached Harry. Al would live. He had lost a few fingers and had some nerve damage, but he would be able to keep using magic, keep moving of his own will, and keep his own train of thought. The other boy was less well off. His leg had been amputated, and the healers still weren't sure what Al had done to the boy's hand. They did know it was very dark magic. Harry requested that as soon as he woke up, Al be tested mentally like James had been years before. He already knew what the result would be.
Al was suspended for the rest of the year. The other boy had detention for the next six months, including over the summer. St. Mungo's told Harry quietly that Albus Severus Potter was dangerous, and if he wasn't looked after, he would end up in Azkaban. Harry nodded slowly, signing his son away to spend the next six months in inpatient therapy, hoping to dampen his raging psychopathy.
How could it have turned out like this?
In the row with Ginny that followed this mess, both of them forgot Harry's approaching physical. Harry only remembered on the day as he was kissing his wife goodbye. As he sat in the waiting room, he picked up a book resting on the table. 'The Medical History of You-Know-Who' it was called. Harry tried to avoid books like that. Many people had approached him for his take on this book or that book about the rise and fall of Voldemort, and he found that if he didn't read them, people stopped asking. But he was bored so he leafed through it.
"Current hypothesis suggests that part of YKW's psychopathy stemmed from his conception under a love potion. This artificial love prevented the emotional centers of his brain from developing properly, resulting in a shifted positive emotional response. This was worsened by his harsh adolescence in a Muggle orphanage."
Pieces started slotting together in Harry's head, but the full picture wasn't revealed until the damning evidence was in his hands. The healer had tested for mind altering drugs as part of his physical, and she had found an old, almost unknown potion in his system. One designed to induce unquestioning loyalty and love to one Ginerva Molly Weasley.
As Harry sat there in shock, Aurors were dispatched to the Potter residence to arrest Ginny under suspicion of potioning her husband. At the same moment, Aurors were dispatched to respond to an altercation at St. Mungo's. One of their long term therapy patients had attacked and killed his minder and was wreaking havoc on everyone in the building. Harry had a nasty feeling he knew who it was.
It took all of Harry's influence to stop the Ministry from executing James. Harry stood in front of Wizengamont and shamed the lot of them. James had done nothing illegal. His only crime was being born under the influence of a love potion. He was adjusting. He was innocent. In the end, the wizarding world rallied behind the Boy Who Lived Twice and James was spared. He was put on an odd modified probation, where he had all of his rights as a citizen but had to check in with the Aurors once a month and attend therapy for the rest of his life.
Albus was not so lucky. His attack on St. Mungo's turned into a massacre, leaving the building in ruins and everyone in it dead. It turned out that he had spent his years at Hogwarts up to that point raising a following, who immediately flocked to his side and launched a war on the wizarding world. Albus was not Voldemort, however, and did not possess the charisma and manipulation technique to keep his movement going. After a few weeks, Aurors had captured most of his followers, leaving him, Scorpius Malfoy, and Katie Bell's son Andrew of all people on the run. Harry himself caught them a week after that in a little wizarding town by the coast, and ended up killing both Al and Scorpius in a massive duel that destroyed most of the town. It was only Harry's quick thinking and skill that kept the battle to two casualties. Andrew was sentenced to 30 years in Azkaban for his crimes. Harry was once again praised as the Savior of the wizarding world.
In her trial, which was open to the public and extremely well attended, Ginny admitted to potioning not only Harry but also most of the boys in Harry's year at Hogwarts as well. Her mother was supplying her and her brother was helping to apply it. Hermione, upon learning that, immediately got tested and divorced Ron. She came back clear, much to her relief. All three involved Weasleys were sentenced to 40 years in Azkaban. Molly died there, but her children came out alive.
Only Lily was spared the rage of the Wizarding World. It turned out that Ginny broke off the potion two weeks before each of Harry's physicals and Lily was conceived in that time. Since she was deemed a normal member of society, she was allowed to continue as she was. However, she had inherited Harry's massive empathy and hated the wizarding world for what it did to James and Harry. The trio ended up fleeing the country after James was attacked in the streets for being a freak of nature, and the Ministry tried to use his self defense as evidence that he was going Dark. They lived out their days on an Unplottable Black island, happy and together.
When Ginny (still Potter) finally got out of Azkaban, she found her husband missing, the vault emptied, and the entire world turned against her. She lived not long after that, miserable and alone.