Launch from Cape Canaveral (KSC); landing on Edwards AFB. Mission ISS-06-5A Lab "Destiny". The launch was scrubbed on January 19, 2001 due to technical problems. This forced a rollback to the VAB for booster separation cable inspection.

Following a two day solo flight the Atlantis docked with the ISS space station on February 09, 2001. Common work with the ISS expedition one was performed. STS-98 delivered to the station the Destiny Laboratory Module.

The first EVA was performed by Thomas Jones and Robert Curbeam on February 10, 2001 (7h 34m). They went to the payload bay of Atlantis where they disconnected cables and removed protective covers from the outside hatch of Destiny. Once at the installation site and after Destiny had been securely installed, the pair began connecting power and data cables.

The second EVA by Thomas Jones and Robert Curbeam occured on February 12, 2001 (6h 50m). They went outside and assisted the robot arm operator with removing the Pressurized Mating Adapter 2 (PMA-2) from the Z1 Truss segment and installing it onto the forward end of the Destiny laboratory. Once that task was complete Thomas Jones and Robert Curbeam moved to a location on the Destiny lab and installed a Power Data and Grapple fixture and video signal converter, to be used with the Canadarm 2.

The third and final EVA by Thomas Jones and Robert Curbeam was conducted on February 14, 2001 (5h 25m). Both spacewalkers attached a spare communications antenna to the International Space Station's exterior. They also double-checked connections between the Destiny lab and its docking port, released a cooling radiator on the station, inspected solar array connections at the top of the station and tested the ability of a spacewalker to carry an immobile crew member back to the shuttle airlock.

Due to bad weather at the Kennedy Space Center the landing was delayed two days and the Atlantis was diverted to the Edwards AFB.