Mongodb agrega tres colecciones

Puede probar debajo de la consulta de agregación.

La siguiente consulta empuja las sections en department cuando se unen y $group para empujar al departamento a crear la estructura final.

db.college.aggregate([
  {
    "$match": {
      "university_id": "5834ecf7432d92675bde9d82"
    }
  },
  {
    "$lookup": {
      "localField": "_id",
      "from": "departments",
      "foreignField": "college_id",
      "as": "departments"
    }
  },
  {
   "$unwind": {
     "path": "$departments",
     "preserveNullAndEmptyArrays": true
    }
  },
  {
    "$lookup": {
      "localField": "departments._id",
      "from": "sections",
      "foreignField": "department_id",
      "as": "departments.sections"
    }
  },
  {
    "$group": {
      "_id": "$_id",
      "name": {
        "$first": "$name"
      },
      "university_id": {
        "$first": "$university_id"
      },
      "departments": {
        "$push": "$departments"
      }
    }
  }
])