In essence it means : things are bad now but I hope things get better later. the stars aligning refers to the astrological idea that when the positions of certain planets sit in defined angles (30 degrees, 90, 45 etc) in relation to the position they had at one's birth then good or bad things will happen. John

"The stars will align" means "good things will happen". It means that "fate will be on your side", this is another way of saying the same thing.