Shanahan began his Rangers career by scoring his 599th and 600th career goals against Olaf Kölzig on October 5, 2006, in a 5–3 season opening win against the Washington Capitals at Madison Square Garden. With assists coming from Petr Průcha on both goals, he became just the 15th player in NHL history to reach the 600-goal mark. Shortly thereafter, on November 14, 2006, Shanahan received the inaugural Mark Messier Leadership Award, an award given monthly to a player selected by Mark Messier who best exemplifies leadership skills on and off the ice. Then, selected to his eighth All-Star Game, he was named captain of the Eastern Conference for the 2007 All-Star Game. On February 1, 2007, he made headlines after expressing frustration in a press conference about his perception that NHL referees are biased against team captain Jaromír Jágr. Later in the month, he was involved in a severe on-ice collision with Philadelphia Flyers forward and former Red Wings teammate Mike Knuble in a game on February 17. Shanahan and Knuble caught each other skating in opposite directions as Shanahan was headed for the bench, at which point Shanahan hit his head on the ice and was left unconscious for ten minutes. He was carried off on a stretcher and taken to hospital where he was released the next day. After missing 15 games, Shanahan returned to the lineup in time for the 2007 playoffs, where the Rangers were defeated by the Buffalo Sabres in the second round. Shanahan completed his first season with the Rangers fourth in team scoring with 62 points in 67 games as an alternate captain to Jágr.