Jomo Hankerson later said that Aaliyah was treated bad over the marriage and that she had a hard time getting her second album to have a producer because of what had happened between her and R. Kelly. With the exception of Sean Combs, he said, there were not too many producers seeking to work with her because people were upset with her, which he did not understand given her age at the time. After the marriage ended, she stopped answering questions about R. Kelly and would often change the subject whenever it was brought up. This was noted by several organizations that did interviews with her. Aaliyah indicated that she would never again work with R. Kelly during an interview with Christopher John Farley, who went on to write a biography of the singer titled "Aaliyah: More Than a Woman". R. Kelly would go on to have more allegations about relationships with underage girls and the relationship with Aaliyah was brought up or mentioned most of the time as a starting point. He refused to discuss his relationship with her and explained his reason for doing this: ""Out of respect for her, and her mom and her dad, I will not discuss Aaliyah. That was a whole other situation, a whole other time, it was a whole other thing, and I'm sure that people also know that." According to her mother Diane Haughton, everything "that went wrong in her life" began with her relationship with R. Kelly. The allegations were dismissed as having little effect on her image or career.
In 1996, Aaliyah left Jive Records and signed with Atlantic Records. She worked with record producers Timbaland and Missy Elliott, who contributed to her second studio album, "One in a Million". She developed friendships with the pair. Timbaland was in love with her, but did not act out on it due to her being years younger than him. Instead he wanted to be a bigger brother figure for her, similar to her own brother Rashad Haughton. However, he struggled with keeping his feelings at bay. During her last days, the pair had an argument and it would be the last time they would speak to each other, as he next learned that she had passed.
She played as herself in the police drama television series "New York Undercover". During this time, Aaliyah participated in the Children's Benefit Concert, a charity concert that took place at the Beacon Theatre in New York.
Aaliyah's first major movie role was in "Romeo Must Die". Aaliyah starred opposite martial artist Jet Li, playing a couple who fall in love amid their warring families. It grossed US$18.6 million in its first weekend, ranking number two at the box office. Aaliyah was scared about bad reviews so she did not look for them. She heard good things about her role in the movie, but there were critics that did not like her role because of her relationship with Jet Li's character not having any realism along with the rest of the movie.
Before she died, she talked to the Isley Brothers about working together, having recorded one of their songs when she was younger during her tenure with Jive Records and was signed to appear in more movies. One of them was "Honey", which came out in 2003 "Some Kind of Blue", a romantic movie and "Sparkle", a movie produced by Whitney Houston that was the remake of the 1976 film of the same name. Houston said after Aaliyah passed that she wanted to be in the movie. Studio officials from Warner Brothers said she and her mother read the script and Aaliyah was passionate about appearing in the movie.
Aaliyah had a vocal range of a soprano. With the release of her first single "Back & Forth", Dimitri Ehrlich of "Entertainment Weekly" expressed that Aaliyah's "silky vocals are more agile than those of self-proclaimed queen of hip-hop soul Mary J. Blige." Aaliyah described her sound as "street but sweet", which featured her "gentle" vocals over a "hard" beat. Though Aaliyah did not write any of her own material, her lyrics were described as in-depth. She incorporated R&B, pop and hip hop into her music. Her songs were often uptempo and melancholy, revolving around "matters of the heart". Her songs have been said to have "crisp production" and "staccato arrangements" that "extend genre boundaries" while containing "old-school" soul music. When she experimented with other genres, such as Latin pop and heavy metal, critics did not like the attempt. As her albums progressed, writers felt that Aaliyah acted more older, calling her progress a "declaration of strength and independence". Stephen Thomas Erlewine of Allmusic described her eponymous album, "Aaliyah", as "a statement of maturity and a stunning artistic leap forward" and called it one of the strongest urban soul records of its time. She portrayed "unfamiliar sounds, styles and emotions", but managed to please critics with the contemporary sound it contained. Ernest Hardy of "Rolling Stone" felt that Aaliyah reflected a stronger technique, where she gave her best vocal performance. Others felt that she was "satisfying rather than extraordinary", stating that she added little to modern R&B.
On August 25, 2001, at 6:50 pm (EST), Aaliyah and various members of the record company boarded a twin-engine Cessna 402B (registration N8097W) at the Marsh Harbour Airport in Abaco Islands, The Bahamas, to travel to the Opa-locka Airport in Florida, after they completed filming the music video for the single "Rock the Boat". They had a flight scheduled the following day, August 26, but with filming finishing early, Aaliyah and her entourage were eager to return to the United States and made the decision to leave immediately. The designated airplane was smaller than the Cessna 404 in which they had originally flown. The whole party and all of the equipment were accommodated on board. As a result, when the aircraft attempted to depart, it was over its maximum takeoff weight by and was carrying one excess passenger, according to its certification. The plane crashed shortly after takeoff, about from the runway. Aaliyah and the eight others on board, pilot Luis Morales III, hair stylist Eric Forman, Anthony Dodd, security guard Scott Gallin, video producer Douglas Kratz, stylist Christopher Maldonado, and Blackground Records employees Keith Wallace and Gina Smith, were all killed.
According to findings from an inquest, conducted by the coroner's office in The Bahamas, Aaliyah suffered from "severe burns and a blow to the head", in addition to severe shock and a weak heart. The coroner theorized that, even if Aaliyah had survived the crash, her recovery would have been virtually impossible given the severity of her injuries. The National Transportation Safety Board (NTSB) report stated that "the airplane was seen lifting off the runway, and then nose down, impacting in a marsh on the south side of the departure end of runway 27 and then exploding in flames." It indicated that the pilot was not approved to pilot the plane he was attempting to fly. Morales falsely obtained his Federal Aviation Administration (FAA) license by showing hundreds of hours never flown, and he may also have falsified how many hours he had flown in order to get a job with his employer, Blackhawk International Airways. Additionally, an autopsy performed on Morales revealed traces of cocaine and alcohol in his system. The NTSB reported that the maximum allowed gross weight of the plane was "substantially exceeded" and that the center of gravity was positioned beyond its rear limit. John Frank of the Cessna Pilots Association stated that the plane was "definitely overloaded".