Instead, the US rewarded supporters of the Iraq War with free trade agreements with Australia and Singapore at the top of the list.
At the time, the differences over Iraq made it seem that any improvement New Zealand-US relations had again stalled.
The nuclear ship issue was once again seen as the main roadblock to the full restoration of ties.
The issue gained particular prominence in 2004 when Don Brash, then the National Party leader, was noted by officials as saying the ban would be "gone by lunchtime" under a future National-led government.
But there were advantages to the diametrically opposed positions over Iraq.
With the US position seemingly crystal clear, New Zealand's wider foreign policy agenda was largely freed up for other matters.
The focus moved to negotiating free trade agreements with other countries following a 2001 model agreement with Singapore and amidst World Trade Organization's ill-fated Doha round of negotiations.
New Zealand's free-trade efforts first bore fruit in 2005 when an agreement was signed with Thailand.
Even more interesting was an agreement signed later that year as a grouping of Pacific Rim countries called the "P4".
The agreement with Brunei, Chile and Singapore was the genesis for what ultimately became the 11-country Comprehensive and Progressive Trans Pacific Partnership (CPTPP).
But New Zealand's biggest prize came in 2008, when it became the first Western country to sign a free trade agreement with China which rapidly became New Zealand's biggest trading partner.
In hindsight, the fallout from the 9/11 attacks and the invasions of Afghanistan and Iraq did New Zealand foreign policymakers a favour.
Afghanistan gave New Zealand an opening to show the US what it had to offer, while Iraq clearly showed New Zealand the limits of that engagement.
Without Iraq, New Zealand might have continued to put even more effort into repairing its US relationship which could have prevented it from moving on to a more diversified trade focus.
But what is even more remarkable is that New Zealand ultimately ended up almost having its cake and eating it too.
Against the backdrop of New Zealand's commitment in Afghanistan, but also with the simple passage of time, the nuclear ship issue that had once seemed so central essentially faded into the background.
Significantly, then Secretary of State Condoleezza Rice called New Zealand an ally in 2008, and diplomatic cables from Wikileaks revealed that US quietly resumed full intelligence sharing with New Zealand in 2009.
New Zealand's defence ties with the US have also largely been restored. Since 2014, New Zealand ships have again fully participated in US-led 'Rim of the Pacific' military exercises.
And in 2016, New Zealand even came within a whisker of securing a free trade deal with the US as part of the CPTPP until Donald Trump withdrew from the arrangement shortly after taking office.
Despite this setback, it is probably only a matter of time until New Zealand concludes a free trade deal of some kind that involves the US.
After all, the US is now taking a much greater interest in New Zealand and its neighbourhood as part of its Indo-Pacific vision that seeks to challenge China's perceived dominance.
Ultimately, the September 11 attacks triggered a chain of unforeseen actions and decisions.
The impact of the tragedy changed the course of US foreign policy.
It changed the trajectory of New Zealand's foreign policy too.
Democracy Project
Geoffrey Miller is the Democracy Projects international analyst and writes on current New Zealand foreign policy and related geopolitical issues. He has lived in Germany and the Middle East and is a fluent speaker of German and Arabic.
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