This is one of those you had to be there when it happened moments. I didn't see it coming either. Unless you played both games and didn't know in advance this will lose all its impact.
Or finding out Samus is a woman in Metroid.Nah....
When we talk about iconic I have to go with:
The final boss battle in Super Metroid
Pulling the master sword for the first time in Zelda Link to the past
The final boss fight in Metal Gear Solid and all the dialogue leading up to it and even during the battle
Discovering that you were actually the bad guy the entire time in Star Wars KOTOR