Otacon's life has been surrounded by computers, and sadly, nuclear weaponry. Her grandfather was a scientist who took part in the Manhattan Project, who later told Otacon of the agony his experience. The fact that he knew his creation was being used as a weapon had caused him great trauma. To add to that, Otacon's father was born on the same day as the A-bombs were dropped on Hiroshima (6th August, 1945), and he was also involved in creating weaponry. It was this shadow that Otacon grew up underneath - and, unfortunately, one she found herself following the footsteps of.
Otacon's father was a big fan of science fiction movies; originally, he had planned on naming his child after the character HAL 9000 featured in 2001: A Space Odyssey. Upon realizing he instead had a daughter, he and Otacon's mother decided upon the name Ada instead. The honour was two-fold: one for Otacon's material grandmother, and one for Ada Lovelace, a historical figure who is widely regarded to be the world's first computer programmer.
Her father eventually divorced Otacon's mother and remarried a British woman named Julie Danziger. Danziger had a child of her own named Emma, and Emma adopted her new stepfather's surname of Emmerich. Ada and Emma became very close. When Ada was a teenager, she was molested by her stepmother, and it continued for years. In 1997, after Hal's father learned of this, he decided to commit suicide by drowning himself in the family pool, dragging Emma in with him. Emma expected her sister to save her, but she didn't know it was happening as she was with her stepmother at the time. Surviving the incident, Emma always claimed to hate her sister, never knowing the truth. Afterwards, Ada, experiencing tremendous guilt for "betraying" Emma and nearly getting her killed, as well as her role in her father's suicide, ran away from home and didn't see any of her family members until several years later.
She dropped out of school but through Internet-based self study, she secured acceptance to the Massachusetts Institute of Technology (MIT), where she earned her PhD at a young age, having earned Bachelor's and Master's degrees previously at Princeton University. During her college years, she devised a solution for the Y2K problem, drawing major attention to herself; even being seen by her contemporaries as the savior of the computer world. It was also around the time that Otacon was harshly reprimanded by her university- and lost her first job- for hacking into the DARPA mainframes- an irony, given her later career.
While studying in MIT, Otacon created a radio-controlled drone mech that she dubbed the 'Metal Gear MK2'. The experiment greatly impressed the FBI, and she was recruited to the Engineering Research Facility. After being caught monitoring and hacking the Bureau's central database, she was forced out of the FBI. Eventually, she joined Armstech.
At ArmsTech, Otacon developed a series of new technologies, including stealth camouflage, that were officially adopted by the US Army. Following this, she became the lead engineer for the Metal Gear REX project. She jumped at the chance to make an actual mech-type robot, which appear frequently in the anime she enjoyed. She was led to believe that it was a mobile defense system, but in reality it was a nuclear doomsday weapon.
In February 2005, Otacon was held hostage by the Sons of Big Boss on Shadow Moses Island, where she was forced to continue her work on REX under heavy guard. During this time, Otacon developed a strong attraction to FOXHOUND member Sniper Wolf, possibly under the effects of Stockholm Syndrome, and was occasionally allowed by her to feed the wolf-dogs on the base.
While confined to her lab, the security detail outside was later eliminated by the Cyborg Ninja, Gray Fox, who then threatened Otacon and demanded to know the whereabouts of his "friend" Solid Snake. In fear of the Ninja, Otacon lost bladder control and urinated on herself and the floor. When Snake interrupted the confrontation shortly thereafter, Otacon hid in a nearby locker while Snake and Fox fought in the lab, spraining her ankle in the process. When Snake finally forced Fox to flee, Otacon reluctantly revealed herself and was shocked to learn the true nature of her creation from Snake, after being interrogated on the subject (as Snake was unaware of Otacon's ignorance of its purpose). Devastated, Otacon realized that she had written yet another chapter in her family's dark history with nuclear weaponry. She decided to take responsibility for her actions, and decided to atone for her mistakes by aiding Snake in his mission, utilizing her stealth camouflage to sneak around the base.
Distraught that Snake would have to kill Sniper Wolf following a snowfield duel, Otacon eventually came to terms with her, herself, and her position in life. Afterwards, she vowed to continue helping Snake with his mission, although she didn't answer radio calls for a short time during her grieving of Wolf's death.
With Otacon's advice, Snake was able to destroy REX and thus defeat the terrorist uprising.
After it was discovered that the Pentagon had sent a nuclear air strike to Shadow Moses, destroying all evidence of what had happened, Otacon decided to remain in the base to aid Snake in his escape. She intended to disable the security locks for the loading tunnel that led outside, nearly sacrificing herself in the process. However, the bombing orders were cancelled shortly before the bombers arrived.
Afterwards, Otacon moved to England for a time, ostensibly because relatives were living there. Following Revolver Ocelot's leaking of REX's schematics on the black market, Otacon and Nastasha Romanenko decide to set up an anti-Metal Gear NGO, Philanthropy. Snake and Otacon soon began a partnership and close friendship, as they would continue to destroy Metal Gear REX derivatives that were being developed by almost every country in the world. During their operations, they also broke into a facility and stole Liquid Snake's corpse, deducing that his corpse might prove useful. During one of their investigations, this time in regards to a U.S. Navy derivative of Metal Gear, Otacon stumbled upon evidence of the Patriots' involvement in the project, although she couldn't find out any more about the organization due to heavy security. She then decided that they should learn more about them in a future operation...
Two years after Shadow Moses, Otacon was forced underground after Snake had been framed by The Patriots during the Tanker Incident. After the Tanker had been sunk by Ocelot, Otacon managed to sail over to the still sinking tanker in a small boat and save Snake, quickly replacing him with the body of the deceased Liquid Snake. Having faked Snake's death, the two of them went underground to continue their anti Metal Gear work outside of the public's watchful eye.
Otacon and Snake eventually came out of hiding after she learned that Emma Emmerich, her stepsister, was working at the Big Shell Offshore Cleanup Facility. Emma secretly informed Ada of the construction of a new Metal Gear weapon deep under the Big Shell's core, and they infiltrated the facility in order to rescue her and stop the project from continuing. Snake disguised himself as Iroquois Pliskin, a junior grade lieutenant in the United States Navy SEALs, while Otacon pretended to be the Big Shell's engineering and systems analyst. After meeting Raiden, Otacon and Snake were able to rescue Emma from the bowels of the Big Shell. They learned that Emma was actually a Patriots engineer, who was hired to build GW and Arsenal Gear because of her genius with AI programming. Emma revealed did it to get back at Otacon, who she felt abandoned her. Eventually, she made up with Emma, and she helped them implant a virus into GW, which they assumed would destroy it. Unfortunately, Emma died shortly afterward due to a fatal knife would inflicted upon her by Dead Cell member Vamp. Despite falling into deep despair over the loss of her sister, Snake encouraged her to move on and rescue all the hostages held in the Big Shell. Otacon was successful, and stayed in contact to support Raiden until he defeated Solidus Snake.
After the Big Shell incident, Otacon and Snake relocated to an unknown location, presumably to ride out the rest of their days fighting Metal Gears.