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Medusa was no stranger to demigods. She personally felt that they were all pawns to the gods. So, it was reasonable to her to be suspicious of the pair of demigods accompanied by three creatures sent by Kronos.
When the group arrived, she allowed them in with caution, fully intending to remain neutral.
If you had asked Medusa who she was expecting to host, she might have said any number of other creatures or immortals. So, it came as a huge shock to her that Kronos would send a demigod who couldn’t have been more than 12.
Perseus Jackson, son of Poseidon, was an enigma; he was young, yet seemed to be in charge of his party. He came in with confidence and borderline enthusiasm, seemingly devoted to the Titan King’s cause. And Medusa knew more than most how callous the gods and immortals are capable of being.
The boy was right about her disdain for the gods, make no mistake; but, Medusa was skeptical of Kronos’ motives and true goals. She did not doubt that the titan would conceal the truth from the young boy. It was this caution that had kept her from engaging thus far, and she had planned on staying neutral.
Perseus ruined these plans. While he was confusing, he was very clearly an immensely powerful demigod; Medusa could see him continuing to grow under Kronos’ tutelage. He also seemed to be astoundingly empathetic, demonstrated through his understanding of her history.
Ultimately, Medusa found Perseus Jackson to be a mortal worth keeping track of. She would align herself with Kronos, in order to keep an eye on the boy. Perhaps she would protect him from harm or abuse. Perseus subverted any and all expectations she would have for a son of the sea god raised by a callous titan.
So, she would allow him to visit and learn from her, and check in on him. Perseus found himself in a den of lions, and Medusa figured he should have a viper in his favor.
Sadly, she wouldn’t get to see him until about a year later.