To unlock Elite Mode, do the following: successfully complete Solo mode on any difficulty setting and thus you will unlock the desired mode.
The following hint will teach you how to return to cell in Ellsworth Penitentiary. First, be quick to return while sneaking out of your cell. Drop the pipe, when on the grating. You mustn’t take it. Now you can go back to your cell. Then, your behaviour should be natural.
To unlock Alternate Endings, you should complete the following tasks:
If you want the ending to be good, you must have your NSA trust above 33%. In addition, save at least two of the three targets (Crouse Ship, Hisham, Lambert).
When you want a normal ending, you should make your NSA trust below 33%. Then, save all three targets (Crouse Ship, Hisham, Lambert). Also you can destroy two targets with your NSA trust above 33%.
At last, to have a bad ending, destroy all three targets (Crouse Ship, Hisham, Lambert) or your NSA trust must be below 33%. In this particular case, you should destroy two of the three targets.