In May, before getting involved with the film, a broken valve caused a depth excursion. Then on 14 June, during the shoot, Houston snagged a tow cable, sinking the tugboat Barcona in the San Pedro Channel near Santa Catalina Island, and drowning a tugboat crewmember. Then, two days later, after filming wrapped, Houston was en route to San Diego, California when she was caught in the net of the fishing boat Fortuna. The nets were destroyed, but no injuries were reported.
On 1 July 1989, Houston left port for a training run. A few days into the training schedule, a standard low-pressure ventilation procedure was conducted at periscope depth. Suddenly and unexpectedly, seawater began flooding from the main air vents. The boat took a sharp up-angle and began driving toward the surface, but lost headway to the weight of the water she had taken on and began to slide backward. Seawater reached the battery compartment and chlorine began to rise from the battery well.
The full power of the Houston’s engines restored headway and drove her to the surface. As soon as she broached, however, she lost her up-angle, and the thousands of pounds of water in her bilges rushed forward. The boat pitched forward, taking on a steep down-angle. Pulled by the weight of the water and pushed by the full power of her engines, Houston dove precipitously.
The engines were reversed in a crash-back maneuver and an emergency ballast tank blow was performed. Houston’s plunge slowed, reversed, and she shot up again, this time remaining on the surface.
Houston returned to port after a long and slow surface transit. The main snorkel valve had failed to close properly. An audible signal that would indicate the valve's opening and closing had been disabled. While eight crewmen were transferred from the Houston, not all left the submarine service.
Houston’s troubles were not over. On 1 August, an electrical fire ignited in the engineering spaces. In September, because of a navigation error, the boat had a close call with a torpedo launched from a helicopter in a training exercise. In November, a navigation error caused the loss of the boat's towed sonar array.
Crewmen aboard the boat during her troubles in the late 80s/early 90s called her the boat from hell; some with affection, some not.
Following a Depot Modernization Period in 1991, the Houston prepared for, and embarked on an incident free deployment to the western Pacific (WEST PAC). With stops in Thailand, Japan, Okinawa and Darwin, Australia, the Houston started to shed her hard luck image.
Upon returning to San Diego in May of 1993, she spent a year in upkeep and training preparing for her next deployment. With a new coat of paint (from a 3 month dry dock stay in the Fall of 1993) Houston deployed again to the West Pac in the Spring of 1994.
This deployment was quickly marred by mechanical difficulties when the ship's aft stern tube bearing failed 6 weeks into the deployment. The Herculean repair involved an in water screw removal and the use of a floating crane towed in from Pearl Harbor Naval Shipyard.
For 9 weeks Houston was stuck in port while a special team from Pearl Harbor repaired the stern tube bearing. With her screw replaced, Houston returned to her at sea duties in late August 1994. The ship returned home to San Diego in time for her crew to enjoy the 1994 holiday season.
In December 1998, Houston was off the coast of southern California during a training exercise when the common discharge flex coupling for the boat's R-12 units ruptured. R-12 is a refrigerant that is used in air-conditioning and refrigeration units. The quick actions of the crew allowed the R-12 to be ventilated overboard while the crew were in emergency air-breathing apparatus (EABs) that protected them from the asphyxiating effects of the gas. A quick stores off-load also saved the perishable foods in the refrigeration compartments. A subsequent and similar rupture happened again in late 1999. These flex-coupling weaknesses have been identified as class problems on Los Angeles-class submarines
Houston was awarded the Battle "E" and engineering "E" in 1998 and Tactical "T"'s in 1999 and 2000.
In May 2000 Houston while transiting between Pearl Harbor, and Yokosuka, Japan, damaged her screw, and had to return to Pearl Harbor for repairs in dry dock. USS Asheville (SSN-758), took over Houston's duties, and completed her planned mission.
In September 2000 Houston lost her anchor while attempting to anchor off the coast of Pattaya Beach, Thailand for a port call. In order for the crew to get a few days of much needed liberty, the crew was divided and took turns steaming the ship around the bay while their counterparts were ashore.
In June 2001 Houston was conducting normal training operations in the Pacific off the coast of Washington state, which included a "crash back" drill, in which the ship goes from ahead flank (maximum forward speed) to back full emergency (maximum engine power in reverse). The maneuver proceeded well, despite the tremendous shaking, noise, and stress the maneuver creates, until the boat began to gain sternway (actually moving backwards through the water).
When a vessel is moving backwards, her rudder and in the case of a submarine, her planes, function in the opposite manner than when she is moving forwards. The stern planesman failed to compensate for this phenomenon, and continued to try to trim the boat as if they still were making headway. When the stern began to rise, he raised the stern planes, which would have depressed the stern if they had been moving forward. While making sternway, it had the opposite effect, increasing the down-angle. The stern continued to rise, more rapidly as the boat accelerated backwards. Before the problem could be corrected, Houston had attained a 35 degree down-angle and her screw broached the surface while still turning at a high rpm. The control team performed a partial emergency ballast tank blow and safely surfaced the boat.
Houston underwent an extensive overhaul at Puget Sound Naval Shipyard in Bremerton, WA, commencing September 2001. The upgrades included reactor refueling, as well as navigation, fire control and sonar upgrades. In December 2004, Houston departed PSNS for her new homeport of Apra Harbor, Guam.
Author Robert D. Kaplan embedded aboard the ship in the spring of 2005 and recounted his experiences in her for his book Hog Pilots, Blue Water Grunts in Chapter Four "Geeks with Tattoos: The Most Driven Men I have Ever Known."