After connecting GET endpoints to the database, you update the rest of your API to use models instead of in-memory data.

For creating data:

app.post('/users', async (req, res) => {
  const user = new User(req.body);
  const savedUser = await user.save();

  res.json(savedUser);
});

For updating data:

app.put('/users/:id', async (req, res) => {
  const updatedUser = await User.findByIdAndUpdate(
    req.params.id,
    req.body,
    { new: true }
  );

  res.json(updatedUser);
});

For deleting data:

app.delete('/users/:id', async (req, res) => {
  await User.findByIdAndDelete(req.params.id);

  res.send('user deleted');
});

Now all operations work with the database instead of temporary data.

This makes your API persistent and usable in real applications.