The best option to you is to use sweet alert, I'm using it in some projects and it's really easy and looks good. Try not to use javascript's confirm... is not very professional
https://limonte.github.io/sweetalert2/
you can download it from there and see some examples. For your problem, sweet alert can do something like this:
swal({ title: 'Are you sure?', text: "You won't be able to revert this!", type: 'warning', showCancelButton: true, confirmButtonColor: '#3085d6', cancelButtonColor: '#5bc0de', confirmButtonText: 'Go to cart', cancelButtonText: 'Continue shopping!', confirmButtonClass: 'btn btn-success', cancelButtonClass: 'btn btn-info', buttonsStyling: false}).then(function () {//redirect to the cart pagewindow.location.assign("/thecartpage.yourextension");}, function (dismiss) { // dismiss can be 'cancel', 'overlay', // 'close', and 'timer'... use cancel to this. if (dismiss === 'cancel') {//Here you close the modal swal().close();}})