There is one scenario that explains everything, including Al's comments at JPM, the on again off again secured note offering, and looming cash shortage.
Possibly the partner and MNKD had met an impass as regards up front financing (to fund through PDUFA), ongoing milestone payments (to fund capacity buildout), and royalty split. If the partner was holding financing hostage to get better royalty terms, MNKD would negate these tactics by raising the funds through secured notes. Once the ppartner realized MNKD was serious, they came back to the table w/ more reasonable terms.
Assuming the partner terms provide adequate funding to carry MNKD through PDUFA and launch, wouldn't you agree that the new shares announced this week are minimally dilutive? Once this deal is announced, wouldn't you expect a "pop" in share price? If the deal is completed in next 6 months, wouldn't Al have been correct on all accounts?
Obviously, this is just one possible explanation, but I like it because it allows us to exist in a world where hero's like Al are real.