The probe will be launched from a Delta rocket in February of 1999. In order to gain enough orbital energy for the long journey to Wild-2, where the comet rendezvous will occur at a distance of about 400 million km from Earth, the spacecraft will effectuate a gravity assist maneuver around the Earth.

When the spacecraft encounters comet Wild-2 in January of 2004, it will have an opportunity to take detailed photographs of its nucleus surface. As it travels through the comet's coma, spewed samples of comet dust will be collected. Stardust will attempt to collect these particles using a special material called Aerogel. The samples will be stored in Stardust's Return Capsule (SRC) which is designed to separate from the main body prior to reentering the Earth's atmosphere. The returned samples will be brought to a laboratory where a thorough chemical analysis can be performed.