Launch from Cape Canaveral (KSC); landing on Edwards AFB. The launch was originally scheduled December 1, 1988, but was postponed one day because of cloud cover and strong wind conditions at the launch site.

Third mission dedicated to Department of Defense. Deploying of reconnaissance satellite Lacrosse (USA-34). Unofficial was reported, that the satellite failed after deployment; Atlantis re-rendezvoused and the crew repaired the payload; that would imply an EVA by Ross and/or Shepherd; Lacrosse was succesful after that.

The orbiter's Thermal Protection System tiles sustained unusually severe damage during the flight. A review panel investigation found that the most probable cause was ablative insulating material from the right-hand solid rocket booster nose cap hitting the orbiter about 85 seconds into the flight as seen in footage of the ascent. The crew made an inspection of the vehicle's impacted starboard side using the robot arm, but the limited resolution and range of the cameras made it impossible to determine the full extent of the tile damage. This was compounded by the fact that the crew was prohibited from using their standard method of sending images due to the classified nature of the mission. The crew was forced to use an encrypted method of sending images. It is believed that this caused the images NASA received to be of poor quality, causing them to think the damage was actually "just lights and shadows". They told the crew the damage didn't look any more severe than on past missions. One report describes the crew as "infuriated" that Mission Control seemed unconcerned. Commander "Hoot" Gibson said in an interview he didn't think the shuttle would survive reentry, even after being told by NASA "The damage isn't that severe." Upon landing, over 700 damaged tiles were noted, and one tile was missing. The tile was located over the dense aluminum mounting plate for the L-band antenna, perhaps preventing a burn-through of the sort that doomed Columbia in 2003.