The last mission has a very long duration, so you do have enough time to go back to base and rearm.
When you are going towards the enemy task force on the campaign map, make sure you are advancing on slow speed, because if you find them on full speed, you spawn into the contact going flank and nearly immediately give away your location.
Fire no weapons until you have identified the boomer. In the mission files, the boomers have their behavior set to 'defensive', which means at the slightest provocation they turn tail and run, and you'll never find them again.
Softly, Softly, Catchee Monke.
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