Apple loaned them the money to build the big factory in Arizona
The original deal was that Apple would loan GT Advanced the money to build the factory, Apple would buy the furnaces to equip it, and GT Advanced would operate those furnaces and sell the sapphire to Apple. Reportedly at full output it would produce 10x more sapphire than all the rest of the factories in the world combined (sapphire doesn't have a huge market, so it isn't as gigantic as Telsa's battery "gigafactory")
GT had an upcoming $350 million payment on this loan, which they can't pay. The question is, is it true Apple was originally planning on using sapphire in the iPhone 6, or was that a rumor? If they were but changed their mind, was it due to GT not being able to deliver what they promised, or due to Apple not being able to use sapphire in the way they originally planned?
They don't lay blame on Apple (yet) so either it wasn't Apple's fault, or they're avoiding accusing them for now, hoping Apple will cut them a break in bankruptcy since they're the major debt holder. Apple might end up owing this factory in lieu of debt repayment, but if so that really won't change much in the relationship, so long as Apple doesn't blame GT for this. If they do, they could contract someone else with sapphire expertise to operate the factory for them, and GT Advanced would probably not emerge from bankruptcy.
Sucks for all those who get caught up in the GTAT stock hype, they've seen the price drop by 95% in less than a month, but that's why they call it speculation not investment!