Not really a bad ending. The feds have no case against him, MIT and JSTOR aren't going to sue him, and JSTOR decided that releasing their archive was a good idea. Hopefully the FBI will drop their case.
35 years in prison is what you would get in federal court for walking across the street as the light was changing from yellow to red. It is there to give the government a better position to offer a plea agreement. It is highly unlikely that he would be convicted of every count, and even if he was, it is highly unlikely that he would receive the maximum sentence for each count.
But, 35 years is scary, and if I were in his shoes and the government said "pay a $100,000 fine", I'd probably agree without much argument. And that's exactly the point of saying he faces "up to" 35 years.
