Eden AI's orders to the crew will be to explore the remains of the PRSS Nuwa. It decided to land in the KYV-2 Crater after identifying the signs of the landing site of the Nuwa. Should humanity continue forth, investigating and establishing contact with the inhabitants of the Nuwa will be crucial.
If Eden AI learns of their fate in the investigation, its next directive will be conflicting. It will desire to find out what happened to EURO-01 like the inhabitants of the Nuwa did, but it will desire for a cautious approach.
If Eden AI learns of the monsters inhabiting the world, it will call for a genetic analysis of their origins, suspecting them to be Alien. Eden AI hasn't been prepared to respond to a situation such as learning of their human origins. It will paradoxically want to protect them, despite their danger to the crew, seeing them as the "humans" they were coded to protect.