First, there was the Red Cross of St. George, the flag of England.
Why a cross? Maybe England secretly wanted to be a Scandinavian state? \_(ツ)_/¯
Some time later, Wales joined England. However, nobody cared about them, seeing as the flag was never changed to symbolize their joining. In fact, even the country's name wasn't changed yet. Poor Wales, forever neglected by the sands of history D:.
Now, Scotland's joining, on the other hand, was much more acknowledged by everyone. The country's name officially became the United Kingdom of Great Britain, and the Scottish flag was added onto the Red Cross of St. George, creating this:
Note that the colors of the Scottish part are changed; the original Scottish flag is a much lighter blue. This is because
obviously the Scottish are horrible at style <which explains the kilt> and thus don't deserve to pick their own colors. As for Wales, they were still completely ignored.
Finally, when Ireland joined, their flag was added in too (sort of), creating the Union Jack we all know to this day.
Of course, if Scotland would leave the UK, the latter would need a new flag yet again. I mean, it would be sort of rude to still claim your rule over a sovereign country in your flag, so yeah. Maybe symbolize the Scottish-English history by just leaving a border on the flag while keeping the inside blank?
The same thing goes for when Northern Ireland (the non-Northern part is already gone) would leave; more edits!
To make matters even more complicated, there are some votes going around for London going independent too. Considering they're pretty much the core of England, this is best symbolized be removing the middle cross too:
However, now we run into a problem: The flag is practically blank! We need more colors! What could we possibly add... AHA! There is one part left of Great Britain (more like Little Britain by now, really) that still has something!