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.
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 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.
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.
Well, Naruto might first try to free Kaguya. He is a hero after all and doesn't like to see anyone chained unjustly. But he would also be very cautious because Kaguya is extremely powerful and was once a great threat. He could try to communicate with her to understand why she is chained there in the first place.
Another scenario could be that Naruto discovers a hidden chamber in the lab. Inside, there are test subjects that Orochimaru was using for his immortality experiments. Naruto feels sympathy for them and tries to rescue them. However, he has to figure out how to deal with the various traps and security measures in the lab first. He might call for help from his friends like Sakura or Kakashi to assist him in this difficult task.