TLDR; Born as Eugene Fitzherbert and orphaned as a young child, he changed his name after his fictional idol 'Flynnigan Rider'. He made a name for himself as a notroious, mostly solitary thief. In a turn of events following years of travel and plunder, however, he experienced a change of heart upon falling in love with Rapunzel, the lost princess of Corona.
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Reccomended fanfiction; One Night in the Top Bunk (NSFW) by Twiggietime
Eugene Fitzherbert was born to King Edmund and his wife as Horace. During Eugene's infancy, the kingdom was corrupted by a powerful opal that threatened to destroy the land. King Edmund ordered for a kingdom-wide evacuation to protect his subjects from the opal's destructive power- including Eugene, who was escorted out of the kingdom by a servant woman and later placed in an orphanage. Eugene never knew the truth of his lineage. He grew up believing that his parents were fearless adventurers traveling the world to make names for themselves. Eugene remained hopeful that once they did, they would return to the orphanage and take him back. In the meantime, Eugene spent all his days with his fellow orphans. His only companion at the time was his lifelong friend, Arnwaldo Schnitz.
Every night, Eugene would read "The Tales of Flynnigan Rider", stories of a rich and dashing swashbuckler who had an abundance of thrilling adventures wherever he went. The more Eugene read it, the more he dreamed of a more audacious lifestyle and decided to break out of his orphan upbringing. Eugene eventually ventured out with Arnwaldo, now known as Lance Strongbow, and grew up into a dashing swashbuckler and gifted horseman under an alias taken from his childhood hero: Flynn Rider. With Lance by his side, Flynn became one of the most infamous thieves in all of Corona, making enemies at nearly every port. He would also plunder regions well beyond Corona, such as Italy, where he learned to speak Italian. Being drawn in more and more by his new ambition and becoming more and more aloof from the people around him, Flynn sought a solitary life of money and freedom, far away.
Apart from Lance (with whom he eventually lost contact), Flynn formed partnerships with other criminals, one of which being a ruthless kingpin known as "the Baron." During their alliance, Flynn developed a relationship with the Baron's daughter, Stalyan. The two were eventually engaged, but Flynn created a bitter enemy in his employer when he left Stalyan at the altar.
Everything Flynn ever wanted, however, quickly lost its appeal in the days he met Rapunzel. When Flynn met the lonesome girl in a remote tower, he was quite irritated to be coerced into taking her to see the Festival of Lights at the kingdom so that he could get back a valuable stolen tiara she had hidden from him. As he spent time with her, he gained a respect for the headstrong young lady that became strong affection and caring. As Flynn cast aside his cares for treasure and solitude he realized his old dream had been replaced by a new one. Flynn fell completely in love with the lost princess and helped her reunite with her parents and reclaim her throne.