Example of querying a GeoJSON feature collection in MongoDB

geo.js

db.test.drop();
db.test.insertOne({
  name: 'Denver',
  location: {
  "type": "FeatureCollection",
  "features": [
    {
      "type": "Feature",
      "properties": {},
      "geometry": {
        "type": "Point",
        "coordinates": [
          -104.9903,
          39.7392
        ]
      }
    }
  ]
}
});

db.test.createIndex( { "location.features.geometry": "2dsphere" } )

const doc = db.test.findOne({
  'location.features.geometry': {
    $geoIntersects: {
      $geometry: {
        "type": "Polygon",
        "coordinates": [[
          [-109, 41],
          [-102, 41],
          [-102, 37],
          [-109, 37],
          [-109, 41]
        ]]
      }
    }
  }
});

print(doc.name);