Unfortunately, by the time they swept the building and congregated the mass of muggles, Malfoy was gone or appeared to be. The other Aurors were pissed about the fruitless bust and told him he'd f'ed up again. They searched the muggles, waited the hour for Polyjuice to wear off and pulled out from the raid. Harry was pissed and was about to leave, too, when he spotted a young child with an old woman shuffling amongst the dispersing crowd. 
Harry felt for the young boy, growing up in a condemned building with other beggars and addicts. But then he noticed platinum blond hair sticking out from under a watch cap and a pointy nose. Harry felt chills down his back... and butterflies in his stomach. His intuition was screaming. Was it Malfoy de-aged? Or something else? He didn't want to say anything, so he released his team and told Ron he was staying. In case there were wards, he Apparated to a nearby roof with vantage points.
He waited over two hours outside the building before he spotted the child and old woman leaving. Several others had left already, but these two looked vigilant and purposely walking. He maintained his distance, following them from above. They walked a few blocks and went into a park. Harry watched as he saw someone in a hoodie and jeans approach them. Harry flicked up a Notice-Me-Not Charm as he silently Apparated near them. It was a handy Auror trick. Then he threw up some Anti-Apparation as he closed in and saw the man pick up the child.
He silently approached and heard, "Thank you for bringing him. Are you okay, my star?" It sounded like Malfoy. 
Harry could just hear the child say, "I'm tired, Papa," 
Harry's eyes widened. Malfoy had a son? 
"I'm sorry, mon cher. I'll take you someplace quiet. Thank you for everything, Madam Jenna," Malfoy said, and handed her money.
"You're leaving, aren't you, Tosh?" the muggle said with a thick accent.
"Yeah, I'm sorry," Malfoy said.
"Take care of yourself and the little bit," she said, patting the boy's head and walking away.
Harry waited until she was gone, before he put up Muggle Repealing Wards and approached Malfoy as he was turning to leave in the opposite direction.
"Malfoy," he called, wand out.
Malfoy's head snapped up. He looked at him and froze, caught like a centaur staring at the night sky. He could see that Malfoy knew he was trapped, caught. No escape this time, though he clearly was considering it.
"Don't try it. I can track you wherever you go now with a Blood Tracker Charm," Harry declared.
Malfoy's shoulders slumped, and his eyes watered. He shook a shaky breath and nodded.
His son seemed to sense his distress. "Papa? Who is that? Are you okay?" 
Malfoy looked at his son, forcing on a smile. "It's okay, mon cœur. It's-It's going to be okay."
However, even his son could hear the panic in his voice. "Papa?!"
Malfoy was seemingly drinking in the sight of his son. "Just remember... what I always tell you." 
His son chanted back, "Papa loves me, and I wuv Papa!"
Malfoy hugged him tightly and glanced at Harry, terrified. He looked so hurt and afraid that Harry felt his own soul ache from his pain. He was almost stuck. Malfoy's eyes filled with tears as he let go to look at his son.
"This is Mister Potter, okay? When you wake up, he'll be there. You need to listen to him," Malfoy explained.
The little boy gasped. "Papa... I will, but-but... what do you mean, Papa!" his little voice shattered as the boy knew something was really wrong.