After The Manhattan Incident, Snake and Otacon disappeared, and lived a quiet life. Sometime after The Manhattan Incident, Raiden was able to rescue Sunny Gurlukovich from The Patriots' clutches, and she was adopted by Otacon and raised into a bit of a computer genius, despite her military lineage. In 2014, thanks to the booming War Economy, Roy Campbell contracted Snake to help eliminate Liquid Ocelot, head of the PMC mother company Outer Heaven. Snake and Otacon reluctantly accepted, and Otacon assisted Snake from his ship the Nomad using Metal Gear Mk. II. Their first mission in the Middle East was a failure after Liquid activated his first test attempt at disabling the SOP system in his PMC troops.
When Snake then infiltrated South America and managed to rescue Naomi Hunter, Otacon rescued them and Raiden using a chopper. Afterwords, aboard the Nomad, Otacon and Naomi Hunter became romantically involved. He also started to not wear his glasses because Naomi commented that he looked "handsome" without them.
Otacon later assisted Snake when they boarded Outer Haven and helped him to dismantle GW which had been restored by Liquid Ocelot. After Liquid Ocelot himself was defeated for good and, Otacon was seen attending the relatively small wedding of Meryl and Johnny Sasaki with Sunny. There, Sunny made friends with a local boy. Otacon saw this and told Sunny that he will allow her to start living on the outside now. It appeared as though Otacon was aware of Snake's plan to kill himself, as he started to cry and explain that Snake wouldn't be back for a long time when Sunny asked where Snake was.
When Snake did not commit suicide, Otacon and him had a short conversation about what they would do now. Otacon said he would gladly stay with Snake and chronicle the remainder of Snake's life as Snake waited to see what the era would bring.
