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Here are the steps to gather user input and store the data in a MongoDB collection within a .mongodb file using JavaScript:

1. Install the MongoDB Node.js driver using npm in your project folder by running the command: npm install mongodb

2. Create a connection to the MongoDB database:

const MongoClient = require('mongodb').MongoClient;
const uri = "mongodb+srv://<username>:<password>@<cluster>/<dbname>?retryWrites=true&w=majority";
const client = new MongoClient(uri, { useNewUrlParser: true });
client.connect(err => {
  const collection = client.db("<dbname>").collection("<collectionname>");
  // perform actions on the collection object
  client.close();
});

Replace the username, password, cluster, dbname, and collectionname with your database credentials.

1. Create a HTML form in your website or application to gather the user input:

<form>
  <label for="name">Name:</label>
  <input type="text" id="name" name="name"><br><br>
  <label for="email">Email:</label>
  <input type="email" id="email" name="email"><br><br>
  <input type="submit" value="Submit" onclick="submitForm(event)">
</form>

1. Write a JavaScript function to handle the form submission:

function submitForm(event) {
  event.preventDefault(); // prevent the form from refreshing the page

  const name = document.getElementById("name").value;
  const email = document.getElementById("email").value;

  // create a new document to insert into the collection
  const newDoc = {
    name: name,
    email: email
  };

  // insert the document into the collection
  collection.insertOne(newDoc, function(err, res) {
    if (err) throw err;
    console.log("1 document inserted");
  });
}

1. Call the submitForm() function when the form is submitted by clicking the "Submit" button.

This will gather the user input from the form, create a new document to insert into the MongoDB collection, and insert the document into the collection. The data will be stored in the .mongodb file for future use.