You will want to get the latest official guidance on this from BGO or Admissions, but in general, at the start of the USNA fall academic year as a 2/C, the final commitment papers are signed. After that point, midshipmen who depart either voluntarily or who are separated for specific reasons (usually conduct/honor/performance), are required to pay back X dollars if they depart with 2 years left, Y dollars (at six figures now, I hear) if they depart with 1 year left or during 1/C year. I'm not sure how academic separations are being handled 2/C year and later, in terms of payback.
The Academy figures two years is a generous time period to figure out whether to stay or go. Plenty of briefs on this topic.
The "Fleet option" has varied over the last few years in terms of whether it's offered. I have observed some prior enlisted personnel returning to the Fleet to complete their obligation at their prior rank. I have seen some midshipmen separated for negative reasons offered the opportunity to go to sea duty for some period of time as an enlisted person (very junior) and then re-apply, if the leadership sees some potential for "rehabilitation." If the reason for separation was the kind that would make service as an enlisted person unacceptable, then monetary payback is the only option.
As with any college, academic transcripts will be available. USNA is an accredited institution similar to civilian colleges. The usual courses will transfer. The professional development classes, such as Navigation, don't.