The NDP's 2003 leadership convention was the first to be determined by a partial "one member, one vote" system in which all members of the NDP were eligible to cast ballots. Blaikie finished second to Jack Layton, who appointed him as Deputy Leader after the convention. As Layton did not have a seat in the Commons, Blaikie also served as the NDP's parliamentary leader until the 2004 federal election. This led to his being sworn in as a member of the Privy Council. He was also named as the NDP's National Defence Critic, and was front and centre in pushing the Liberals to not participate in the Iraq War, in opposing Canadian participation in ballistic missile defence, and in asking questions about the rules of engagement and changing role of Canadian troops in Afghanistan.