best way to travel from Barcelona to Mont Saint Michel with a stop in Basque country

The short answer is that there doesn't even seem to be a decent way, much less a "best way". I imagine you already know that driving from Barcelona to Mont-St-Michel would subject you to an extremely high international drop fee for the rental car. ViaMichelin estimates the direct drive at 630 miles and about 12 hours. That doesn't get you anywhere near the Basque Country, and of course the time estimate doesn't include any stops or the time you'd spend at the two rental-car offices.

The direct train route takes about 10-1/2 hours and doesn't go through the Basque Country. It requires two changes, one of them a cross-town switch of rail stations in Paris. The rail connection between Barcelona and the Basque Country isn't particularly fast, so inserting that area into the routing is going to do ugly things to the total travel time. If you force a stopover in San Sebastian, the travel time increases to 34 hours. Stopping in either Bayonne or Biarritz produces a trip of over 30 hours.

I didn't bother to look at flights, because I can't imagine you want to spend two days in a total of three airports in exchange for a tiny number of hours in the Basque Country. If you want to explore flying, try skyscanner. Bilbao's airport is busier than San Sebastian's. The most useful airport on the French end would probably be Rennes. Rennes is an attractive city, so if you decide the Basque Country stopover isn't practical, you might consider flying from Barcelona to Rennes (I assume you'll need to make a connection), seeing a bit of Rennes and staying there overnight, then going on by train and bus the next day.

"Best" is one of those words no one can answer but you.

For me, the best solution would be to not jam these 3 destinations together in the first place.

You can fly Barc > San Sebastian. Here are some options for the next leg of that trip.
https://www.rome2rio.com/s/Donostia-San-Sebasti%C3%A1n/Rennes

I hope that gives you an idea of the possibilities. "Best" is your call.

@ acraven Thank you. Yes, I agree - will probably fly to Rennes. I don't think I can cram a Basque visit on this trip.

@ Adam Thank you. I think it's probably futile to add a stop to Basque country, this trip. I will most likely fly from Barcelona to Rennes.