Logan arrived in town to visit his old army buddy, Cooper Barrett. He started a flirtation with Lulu Spencer and Cooper's girlfriend Maxie Jones. After some investigation, Lulu came to suspect that Logan was the son of Scott Baldwin. Logan later admitted that he'd known Scott was his father since he was a kid, and said that Scott had ruined his family with a bad business deal years before. Because of this, Logan immediately clashed with Scott. In September, Logan and Scott agreed to a DNA test, which confirmed that Scott and Logan were indeed father and son. Since then, Scott and Logan started to improve their relationship.
In early 2008, Scott and Logan's relationship appeared to be going well when Logan asked Scott, getting a job. However, their relationship deteriorated again when the file containing the DNA results for Georgie Jones' murder was stolen off the police commissioner's desk. Scott accused Logan of taking the file to blackmail Johnny Zacchara into staying away from Lulu, as Johnny was a suspect in Georgie's murder. Logan denied it, and angrily told Scott not to bother him again, and that he was glad that he had stayed out of his life as a child. Meanwhile, Logan had started to stalk Lulu, determined to win her back.
On July 8, 2008, Lulu witnessed Logan attack Maxie Jones, who he blamed for his and Lulu's breakup. When Logan tried to explain to Lulu, he became violent and was killed when she stabbed him in self-defense, which Maxie, Johnny Zacchara and Claudia Zacchara (unwittingly) helped cover up. Scott was devastated and out for blood. He was the prosecutor in Johnny's trial for Logan's murder, despite being the victim's father. He used several dirty tricks to get Johnny the death penalty, including fraud by forging papers stating that Logan had been working undercover for the PCPD, and calling an unstable Lulu to the stand. Scott was outraged when Johnny was acquitted. When Scott discovers that Lulu was the one who killed Logan, he starts terrorizing her, sending her anonymous letters while she is in Shadybrook. He eventually goes to confront Lulu and threatens her with lethal injection when Lulu's mother, and Scott's childhood love Laura Spencer wakes up from a catatonic state to defend her daughter.
In 2013, a now engaged Scott and Laura return to Port Charles, and Scott and Lulu agree to put the past behind them.