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Okay, so this has happened twice. First, when I was about to enter Page's bunker (or somewhere around there). The loading screen ended and I was taken to the title screen. Today, I had finished getting the New Dark Ages ending and I was on my way out of the control room, and instead of seeing the ending cinematic I was taken to the PS2 browser/system configuration screen. Interestingly, I clicked the browser option and the game disc didn't show up.
I'm guessing it's just my disc. I restarted and finished the game shortly after. So anyone else encounter this?
I have never encountered this problem with Deus Ex, but I have with other games. Usually a good cleaning of the laser disk reader in the PS2 and/or cleaning of the game disk's scratches will help. The console "loses" the game because it has trouble reading it when it loads things, so that's why your loading screens seem to be screwing up.
Take a look at a few forums or youtube videos to find the best way to clean your PS2's guts, just to be safe.