Linguistics map of the Iberian Peninsula 1000-2000 AD
When language isolates are discussed, people often assume they are some weird, unique language that just sprung out of nowhere. It’s much more likely that these languages (like Basque) were parts of must larger families that died out. In this gif, you can see how Castilian overwhelms Iberia, which had been primarily speaking Arabic - Mozarabic. Even at that time, Basque was already a fairly small language. So what did the language landscape look like before Arabic - Mozarabic was the dominant language family?
I don’t know, but language has been around a lot longer than we have historical accounts, and it’s reasonable to think that Basque’s language family was once spoken in a much wider area. Who knows, maybe it originates from a language family that dominated Europe before Germanic and Romance languages existed. In any case, we no longer can trace it back to connect it to the languages in Europe today.