Thanks for the query.
The "Union Jack" or The "Union Flag" or the British Flag is a composite design made up of three different National symbols.
1. St. George's Cross, The Flag of England
2. St. Andrew's Cross, The Flag of Scotland
3. St. Patrick's Cross, The Flag of Ireland
The blue color comes from the Flag of Scotland, St. Andrew's Cross, which is a white diagonal cross on blue background. The Flag of Scotland itself had evolved from light blue to dark blue and sometimes navy blue background. The dark blue background was probably selected on the basis of durability of darker dyes.
More detailed information can be found here -
http://www.know-britain.com/general/union_jack.html
https://en.wikipedia.org/wiki/Flag_of_Scotland
