If I recall correctly, you need to go back to the cafe and Nanami will be missing. One of the girls there will tell you she lives near the park. Going to the park after school will let you meet up with Nanami.
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I don’t know the exact triggers but the main story content needs finding and speaking to Kari in the lab and Yuri in the mansion. Additional content is triggered by choosing dialogue options when talking to them in and after school. That should lead to the girls all visiting your house. I don’t know if the sleepover at Yuri’s is required before Nanami goes missing from the cafe.