Launch from Cape Canaveral (KSC); landing on Edwards AFB; ISS-13A ITS-S3 / ITS-S4. The launch was originally planned for March 15, 2007 but postponed due to damage from a hail storm on February 26, 2007.

Atlantis, delivered to the International Space Station (ISS) the second starboard truss segment (the S3/S4 Truss) and its associated energy systems, including a set of solar arrays. During the course of the mission the crew installed the new truss segment, retracted one set of solar arrays, and unfolded the new set on the starboard side of the station.

Following a two days solo flight the Atlantis docked to the ISS on June 10, 2007. During the next nine days the crew permoned common work with the ISS expedition 15. Clayton Anderson was transferred to the ISS and Sunita Williams to the crew of STS-117 for returning to the Earth.

The first EVA was performed by James Reilly and John Olivas on June 11, 2007 (6h 15m) for hooking up power cables to begin activation of the S3/S4 truss and starting to prepare the Solar Alpha Rotary Joint, also known as the SARJ, for activation. The work included connecting power, data and cooling cables between S1 and S3; releasing the launch restraints from and deploying the four solar array blanket boxes on S4 and releasing the cinches and winches holding the photovoltaic radiator on S4. They also rotated the keel pin on S3; rigidized four Alpha Joint Interface Structure struts and installed one Drive Lock Assembly on the Solar Alpha Rotary Joint; and at least removed some of the SARJ launch locks and restraints.

The second EVA by Patrick Forrester and Steven Swanson occured on June 13, 2007 (7h 16m) to continue the activation of the S3/S4 and assist in the retraction of the starboard solar array on the Port 6 (P6) truss. They removed all of the launch locks holding the 10-foot-wide solar alpha rotary joint in place, but were not able to remove the joint's launch restraints as well; they left them for a later spacewalk. After the end of the spacewalk problems become serious when navigation computers in the Russian segment did not operate. Over the next days, the computers were repaired. Meanwhile Mission Control had decided to extend the mission duration.

The third EVA by James Reilly and John Olivas was conducted on June 15, 2007 (7h 58m) to finish removing the SARJ's launch locks and restraints so that it can be activated and repairing a raised corner of a thermal insulation blanket on the shuttle's left Orbital Maneuvering System pod that came loose from the shuttle during launch.

The fourth and unplanned spacewalk was performed by Patrick Forrester and Steven Swanson on June 17, 2007 (6h 29m) to activate the new solar array rotation mechanism SARJ and ready the lab complex for a critical sequence of upcoming construction flights; work included the removal of a keel pin and drag link from S3, the complete bolting down of a piece of debris shielding on the Destiny laboratory, the installation of a computer network cable on Unity, and the removal of a Global Positioning System antenna.

During the separation from the station, a camera in the cargo of Atlantis bay observed numerous objects what could have been harmless pieces of ice and one much larger, more distinct piece of debris slowly floating away. It was not clear whether the objects originated from the shuttle or the space station. Around 21:30 UTC, Commander Frederick Sturckow reported yet another piece of debris leaving the area of Atlantis. Frederick Sturckow identified them to the mission control in Houston as "little phenolic-looking, kind of tan-looking washers with four slots" that are used to tie down the Multi-Layer Insulation blankets in the payload bay.

The landing was running a day late because of blustery Florida weather.

Clayton Anderson landed on November 07, 2007 at 18:01 UTC with STS-120.