Any deployment is a challenge, and this was no exception. Early in the WESTPAC deployment, port visits in Hong Kong and Singapore were cancelled due to weather delays. An F/A-18 crashed into the sea, and the pilot was lost. While she was in the western Pacific, the carrier was ordered to the Arabian Gulf at best speed, so a planned port call in Thailand was skipped. In the Arabian Gulf Lincoln and her battlegroup relieved the George Washington battlegroup, and flew nearly 1,500 sorties over Iraq.

This was a particularly challenging trip to the Gulf, as Lincoln was in the region when USS Cole was attacked by terrorists at Aden, Yemen. The attack raised tensions and alert levels, forced cancellation of port calls, and sent ships from around the region rushing to Aden to assist Cole. One ship from the battlegroup, USS Paul Hamilton (DDG 60) was called upon to escort the deckship M/V Blue Marlin from Dubai to Aden, where the deckship loaded Cole for transport back to the US.

After 90 days in the Arabian Gulf, Lincoln finally headed home, stopping in Australia for well-deserved liberty after 77 consecutive days at sea.