You could do one of two options
- SLA System - lead has to enter the flow based on Lead Status=MQL, then Wait 90 days. If Not Member of List with Activity, then Lead Status=X.
- Run batch
- if Lead Status=X and Not Activty Was Logged IN PAST 90 days, then Lead Status=X
- run every day, but lead can only enter once or every 90 days.
I feel there is a confusion here: you can only create a trigger on something that happens. So you cannot create a trigger on absence of activity
In your case, look for batch approach as described by Josh.
Another possible angle to take this would be to make a process in SF that changes the field's value.