class Comment(db.EmbeddedDocument):
    ...
    visibility = db.IntField(default=0)
    mentions = db.ListField(db.GenericReferenceField())


class Message(db.Document):
    ...
    comments = db.ListField(db.EmbeddedDocumentField(Comment))



# I want the list of Messages that have comments that ment a particular user and they are visible (the comments):

user = User.objects.get( ... )
Message.objects(__raw__={'comments': {'$elemMatch': {'visibility': 0,'mentions': {'_cls': 'User', '_ref': user.to_dbref()}}}})