One secret could be the formula for a super - strong chakra - enhancing potion. This would give him an edge in battles against tough opponents.
He could uncover secrets about his family. There might be some hidden records in the library that reveal things about his father or mother that he never knew before.
He might uncover a hidden weapon that could change the balance of power in the ninja world.
The lab could hold secrets about Orochimaru's past. Maybe there are records of his early days as a ninja, his training, and what led him to become so obsessed with immortality. Naruto might stumble upon these records and gain a better understanding of his enemy.
He might discover some long - lost jutsu. Ancient labs could hold secrets to powerful ninja techniques that have been forgotten over time. Maybe he'll find scrolls with unique chakra - based abilities or old - fashioned weapons with special powers.
One interesting take in a fanfiction could be that Naruto finds Orochimaru's lab while looking for Sasuke. He enters the lab full of determination to bring Sasuke back. Inside, he sees the remnants of Orochimaru's attempts to transfer his soul or create powerful hybrids. This discovery makes Naruto realize the full extent of Orochimaru's madness and the danger Sasuke is in. It also gives him more motivation to not only rescue Sasuke but also put an end to Orochimaru's evil plans once and for all.
He may find rare ninja tools. These could be weapons or items with special abilities that no one has seen in centuries. For example, a sword that can cut through any defense or a tool that can enhance one's chakra.
Perhaps the scroll has a connection to the Sage of Six Paths. Since many important things in the Naruto story are related to the Sage, it could be that the scroll contains some of his teachings or prophecies. Naruto, being the protagonist, might be the one destined to uncover and fulfill whatever is written in the scroll.
He could uncover the truth about his father's real mission before he died. Maybe it was something that was kept hidden from the village for some reason.
He might discover some new and powerful jutsu hidden there. Maybe it's a lab created by an ancient ninja clan that was lost to history.
Well, Naruto would probably immediately try to free her. He's the kind of person who can't stand seeing someone in distress. He might use his ninja skills to break the chains quietly if he's worried about enemies nearby. Then he'd likely ask her who she is and how she ended up there.