Continuity mistake: At the very end of the episode when Nina Sharp exits the elevator, she mostly steps out of the elevator completely before the masked men come and shoot her. However, when they review the security footage of the attack in the next episode, "There's More Than One of Everything," you see that she barely takes a step before being shot. (00:49:15)
Continuity mistake: When Olivia crosses over to the other side you see people wearing FBI jackets. But according to later episodes that had changed to Fringe Division on the other side years earlier.
Answer: He helped his father evade capture, impeding the investigation.