Launch from Cape Canaveral (KSC); landing at Cape Canaveral (KSC); ISS ULF-3 ELC-1 ELC-2.

The payload bay carried two large ExPRESS Logistics Carriers holding two spare gyroscopes, two nitrogen tank assemblies, two pump modules, an ammonia tank assembly, a spare latching end effector for the station's robotic arm, a spare trailing umbilical system for the Mobile Transporter, and a high-pressure gas tank. STS-129 was the first flight of an ExPRESS Logistics Carrier.

Following a two day solo flight Atlantis docked to the ISS on November 18, 2009. Joint operations with the ISS expedition 21 were performed. Nicole Stott was transferred to the STS-129 crew for returning to the Earth. She was the last ISS crewmember returning by a Space Shuttle.
Robert Thirsk from CSA was originally slated to return from his stay aboard the station with STS-129, but due to flight delays, it was announced that Nicole Stott and Robert Thirsk would swap return seats, with Nicole Stott returning aboard STS-129, and Robert Thirsk returning on Soyuz TMA-15.

On flight day 3 a few hours after docking Leland Melvin and Randolph Bresnik removed the Express Logistics Carrier 1 (ELC-1) from Atlantis' payload bay and handed it off from the shuttle robotic arm to the station robotic arm controlled by Barry Wilmore and Jeffrey Williams. They installed the carrier on the station's Port 3 truss.

The first EVA was performed by Michael Foreman and Robert Satcher on November 19, 2009 (6h 37m) to install a spare antenna on the station's truss, or backbone, and a bracket for ammonia lines on the Unity module. They lubricated the grapple mechanism on the Payload Orbital Replacement Unit Attachment Device on the Mobile Base System and lubricated the snares of the hand of the station's Japanese robotic arm. This work was done earlier than planned. They used this time for deploying the Payload Attach System (PAS) on the Earth-facing side of the Starboard 3 truss, the crew had difficulty loosening a bolt and removing a diagonal brace on the PAS. After hammering on a bolt and wiggling the brace, they successfully deployed the PAS and reinstalled the brace. This additional work was originally planned for EVA 2.

Prior to the second spacewalk Atlantis robotic arm operators Leland Melvin and Robert Satcher lifted Express Logistics Carrier 2 (ELC-2) out of the shuttle payload bay. The shuttle arm handed off the carrier to the International Space Station robotic arm, which installed it on the Starboard 3 segment of the station’s truss. The nearly 14,000 pound carrier contains spare equipment that will help prolong the lifetime of the space station.

The second EVA by Michael Foreman and Randolph Bresnik occured on November 21, 2009 (6h 08m) to install the GATOR (Grappling Adaptor to On-Orbit Railing) bracket to the Columbus laboratory and an additional ham radio antenna. They installed on the truss an antenna for wireless helmet camera video. They also relocated the Floating Potential Measurement Unit that records electrical potential around the station as it orbits the Earth and deployed a bracket to attach cargo on the truss.

The third and final EVA by Robert Satcher and Randolph Bresnik was performed on November 23, 2009 (5h 42m) to install a new oxygen tank on the Quest airlock and the next set of the "Materials on International Space Station Experiment," known as MISSE-7A and 7B, on ELC-2. They worked the heater cables on a docking adapter in advance of the Tranquility node's installation on Unity's port side and deployed another cargo platform on the truss.