Board Thread:Questions and Answers/@comment-80.3.69.25-20131123085136/@comment-1210805-20131123101340

I'll answer this with the assumption that Rising is your first Metal Gear game. Sunny is the daughter of the MGS2 character Olga. Olga was the daughter of Sergei Gurlukovich and when he died she became the leader of his private mercenary army. At the time of her father's death she was pregnant with Sunny. She gave birth to Sunny in the two year gap between that event, and the Big Shell incident in which Raiden undertook his first real mission (other than what he did as a child soldier). The Patriots (the organisation controlling events from the shadows) kidnapped Sunny in order to force Olga to act as their agent.

During the Big Shell incident Olga was forced to work against her own mercenary group and help Raiden. If Raiden died then the Patriots would kill Sunny. Olga also teamed up with Snake during these events and after her death, Snake and Raiden were both determined to rescue Sunny. Raiden eventually got help from the Paradise Lost army and managed to free Sunny but was captured in the process. Raiden was held by the Patriots who experimented on him and turned him into a Cyborg.

During her time as a prisoner of the Patriots, Sunny was kept indoors and interacted mostly with computers. According to Rising the Patriots also likely conducted experiments on her. All of this lead to Sunny being a child genius but socially awkward. Once free Sunny was left in the care of Hal "Otacon" Emmerich (who she refers to as uncle Hal, and would at some point be adopted by) and Solid Snake. She was instrumental in bringing down the Patriots' AI system and setting up the future.

Due to Raiden's rescuing of her, and what they did to him, Raiden and Sunny have a special bond and are quite protective of one another (Sunny carries a lot of guilt over what happened).