STS-93 in 1999 marked the 95th launch of the Space Shuttle, the 26th launch of Columbia, and the 21st night launch of a Space Shuttle. Eileen Collins became the first female shuttle Commander on this flight. Its primary mission was to launch the Chandra X-ray Observatory, the heaviest payload ever carried by the Space Shuttle system, at 22,780 kilograms (50,222 lb).

STS-93 would be Columbia's last mission until March 2002. During the interim, Columbia would be out of service for upgrading and would only fly again on STS-109. The launch was originally scheduled for 20 July, but it was aborted at T−7 seconds. The successful launch of the flight occurred three days later.

During the main engine ignition sequence, a gold pin used to plug an oxidizer post in the Space Shuttle's number three (right) engine came loose and was violently ejected, striking the engine nozzle's inner surface and tearing open three cooling tubes containing hydrogen. These ruptures resulted in a leak upstream of the main combustion chamber. This anomalous event and the automatic response to the leak by the right engine's controller did not violate any launch commit criteria and liftoff proceeded normally. However, approximately 5 seconds after liftoff, an electrical short disabled the center engine's primary digital control unit, DCU-A, and the right engine's backup unit, DCU-B. The center and right engines continued to operate on their remaining DCUs for the rest of powered flight to orbit. The redundant set of DCUs in each engine controller saved Columbia and her crew from potential catastrophe, as shutdown of two engines at that point in the flight would have resulted in a very risky contingency abort with no guarantee of success. The electrical short was later discovered to have been caused by poorly routed wiring, which had rubbed on an exposed screw head. This wiring issue led to a program-wide inspection of the wiring in all orbiters.

Because of the leak in the right engine, its controller sensed a decrease in power or thrust—measured indirectly as main combustion chamber pressure—since the leaking hydrogen was not being burned in the SSME's two pre-burners or the main combustion chamber. To bring the engine back up to the commanded thrust level, the controller opened the oxidizer valves a bit more than normal. The hydrogen leak and increased oxidizer consumption resulted in the right engine deviating from the desired oxygen/hydrogen mixing ratio of 6.03 and running hotter than normal. The increased oxidizer consumption during ascent resulted in a premature shutdown of all three engines near the end of the projected burn due to low liquid-oxygen level sensed in the External Tank. Though the premature shutdown resulted in a velocity 15 ft/s (4.6 m/s) lower than targeted, the vehicle safely achieved its intended orbit and completed the mission as planned. This incident brought on a maintenance practice change that required damaged oxidizer posts to be removed and replaced as opposed to being intentionally plugged, as was the practice beforehand.

Three days previously, in the first launch attempt, the launch was stopped at T−7 seconds, just prior to the SSMEs' ignition sequence, due to a senior console operator manually triggering a cutoff in the countdown. It was later determined that the console operator, monitoring the hydrogen gas concentration in the Space Shuttle's aft compartment, where the three SSMEs are located, saw a hydrogen increase spike above the Launch Commit Criteria redline, for a single sample just prior to main engine start. Subsequent troubleshooting and analysis indicated the most likely cause was the mass spectrometer instrument experienced a data anomaly in the high vacuum region of the instrument for a single sample. The system performance was nominal prior to the cut-off and during subsequent launch attempts.

The primary objective of the STS-93 mission was to deploy the Chandra X-ray Observatory (formerly the Advanced X-ray Astrophysics Facility) with its Inertial Upper Stage booster. At its launch, Chandra was the most sophisticated X-ray observatory ever built. It is designed to observe X-rays from high energy regions of the universe, such as hot gas in the remnants of exploded stars.

Other payloads on STS-93 included the Midcourse Space Experiment (MSX), the Shuttle Ionospheric Modification with Pulsed Local Exhaust (SIMPLEX), the Southwest Ultraviolet Imaging System (SWUIS), the Gelation of Sols: Applied Microgravity Research (GOSAMR) experiment, the Space Tissue Loss – B (STL-B) experiment, a Light mass Flexible Solar Array Hinge (LFSAH), the Cell Culture Module (CCM), the Shuttle Amateur Radio Experiment – II (SAREX – II), EarthKAM, Plant Growth Investigations in Microgravity (PGIM), the Commercial Generic Bioprocessing Apparatus (CGBA), the Micro-Electrical Mechanical System (MEMS), and the Biological Research in Canisters (BRIC).

The Shuttle Ionospheric Modification with Pulsed Local Exhaust (SIMPLEX) payload activity researched the source of Very High Frequency (VHF) radar echoes caused by the orbiter and its OMS engine firings. The Principal Investigator (PI) used the collected data to examine the effects of orbital kinetic energy on ionospheric irregularities and to understand the processes that take place with the venting of exhaust materials.