ooc!History
Otacon's life has been surrounded by computers, and sadly, nuclear weaponry. His 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 this, Otacon's father was born on the same day as the A-bombs were dropped on Hiroshima (6th August, 1945). (Although it's not directly mentioned, one could assume that Otacon's father was also a scientist-- in a cutscene during Metal Gear Solid 3: Snake Eater, a picture is shown: Grenin, along with a person that looks closely like Otacon. As this is way before his time, it hints that someone in Otacon's family had a tie with weapons development in the 1960's)
Otacon himself did not attend school- he studied via online courses, matriculating at the Massachusetts Institute of Technology (M.I.T). In his early twenties, he earned his Ph.D, having earned Bachelor's and Master's degrees at Princeton University. During his college years, he came up with a solution for the Y2K problem, drawing major attention to himself; even being seen by his contemporaries as the savior of the computer world. It was also around this time that Otacon was harshly reprimanded by his university- and lost his first job- for hacking into the DARPA mainframes- an irony, given his later career.
While studying in MIT, Otacon created a radio-controlled drone mech that he dubbed the Metal Gear MK2. This experiment greatly impressed the FBI, and he was recruited to the Engineering Research Facility. He later joined Armstech and developed Metal Gear Rex as a Mobile Theater Missile Defense (MTMD)- which he did not realize the full purpose of.
While making his way though the Shadow Moses facility, Solid Snake has to locate Otacon on base, who by that time was the team leader of the Rex project. As Snake meets up with him, Otacon learns of the true nature of REX- the completion of a rail gun unit and the installation of a new nuclear warhead. He finds himself caught in the same trap his grandfather was- caught between his interests as a scientist, and the idea that his technology was meant to be used to kill thousands of innocents. Driven by this, Otacon agrees to assist Snake, giving him his frequency for support. He assists Snake by providing a means of escape for the soldier, and giving him information about the base.
Additionally, he encounters Snake at one point with an odd question- "Can love bloom on a battlefield?" Although a bit incredulous, Snake says it's possible, as long as one can protect the person they love. This leaves an impression on Otacon, who agreed to this. We learn that Otacon was smitten with one of the antagonists, Sniper Wolf (though whether this is due to Stockholm's syndrome or not is debatable), whom Snake must fight. Although he pleads with Snake to not fight her, the combat goes on, leading Sniper Wolf to her death, leaving Otacon in a tearful state.
Eventually, as Snake goes on to defeat Liquid and save Meryl, Otacon decides to stay behind and ensure that security is disabled-- despite the fact that Shadow Moses was about to be bombed to cover up the problems there. Impressed with Snake, Otacon was gladly willing to stay behind and sacrifice himself to help Snake and Meryl escape. At the end of the game, as the bombing is called off, Snake asks Campbell to send out a chopper to retrieve Otacon at the base, thus helping him escape.
Not much is known between the events of Metal Gear Solid and Metal Gear Solid 2: Sons of Liberty. According to interviews with Hideo Kojima, Otacon and Snake went their separate ways, with Otacon returning to England for six months. He, along with Natasha Romanenko, founded the anti-Metal Gear group Philanthropy, a fringe U.N. organization. Otacon travels to Alaska to convince Solid Snake to join the group, to which Snake agrees. It's assumed that from here to the Tanker chapter in MGS2, the two men worked together in Philanthropy- Snake doing the field work, while Otacon worked support/intel via CODEC. As they worked together, it's also assumed that they grew close, becoming best friends by the Tanker Chapter.
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 he learned that Emma Emmerich, his stepsister, was working at the Big Shell Offshore Cleanup Facility. Emma secretly informed Hal 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 an important Big Shell engineer. After meeting Raiden, Otacon and Snake were able to rescue Emma from the bowels of the Big Shell and reunite the two. 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- she did it to get back at Otacon for abandoning her. Eventually, he made up with Emma, and she helped them implant a virus into GW, which they assumed would destroy it, but she 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 his sister, Snake encouraged him to move on and rescue all the hostages held in the Big Shell. Apparently he was successful in this, 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. And that's where our new story begins...