Basically, there's another group of people who are living out on the Skyway. But they aren't on the best terms with the people who made the Bastion, which is why communicating with them has been iffy at best so far.

Think of it like how different countries don't always get along, and sometimes they might go to war with each other, and how two countries just ended a war not too long ago but now one country needs the help of the one they had been fighting with.