To get a secret 5th ending to the game do the following:

Firstly, make sure that you haven't uploaded the Aquinas information to anyone yet. Enter UNATCO and when you come to the ruined wall pick up the flag on the left. Continue through UNATCO (while holding the flag) and go down the stairs to the floor below (the middle floor not the bottom one). Enter the room on the far left of the hallway(Manderley's old office for those who played the original Deus Ex) and continue through the office and into the bathroom. While holding the flag flush the toilet and you should get a message saying 'The REAL endgame'. You will be transported to a nightclub where you will find various characters dancing and a number of Quote Files floating about.

N.B. This is one-way so make sure you save before doing it.