Varuna had been traveling with Ryuga since after the finale of Battle Bladers, and through their journeys, she grew a deep feeling of respect for the so-called Dragon Emperor, including affection. She taught him the basics of living alone in the wild, such as swimming, hunting, fishing, and gave him advice about blading. It was difficult dealing with his hot-tempered attitude, but over a long time, it seemed like he mellowed out and had finally gotten used to her. They still had heated bickering over control in battles, but they came out as a fierce and dangerous duo with Ryuga's powerful strength and Varuna's intelligent strategies.
However, Varuna portrayed somewhat slightly obsessive or possessive behavior due to her increasing interests in Ryuga. Despite her usual calm and kind demeanor, she had feelings of jealousy and insecurity when around others and not with Ryuga. She could not stop thinking about him for days.
Eventually, she has noticed the signs herself and became extremely troubled, wondering if Ryuga noticed them as well. She has fallen for him, and it was affecting her more than when she first joined him. Because of this realization, she feared for her relationship with Ryuga and decided it is time that he is ready to live on his own.
*This is part of Varuna's Story, months before Metal Fury*