I recently watched the English version (http://www.youtube.com/watch?v=pExn-S7WduQ&feature=related) of the Giovanni event battle in HG/SS and noticed a few extremely noticeable quotes and a mysterious noise.
After Giovanni trembles (literally) from defeat and makes his leave, the normal *walking out cave* sound effect isn't heard, and instead there is this *SPLASH* sound followed by dead silence. As Giovanni's secret hideout was in Tohjo Falls, the entrance was directly next to the rapid waters and he could've committed (or atleast) suicide.
After the *SPLASH* sound, the radio signals in from the Goldenrod Radio Tower Team Rocket members "Where has Giovanni gone? I wonder if he's coming..." As if to give you the assumption that he has forever vanished.
Ethan: "They keep calling their boss. I feel sorry that they don't know he's not coming".
Giovanni never told Ethan or the protaganist that he won't go to Goldenrod, how did Ethan know?
Does anyone agree with me that Giovanni might've committed suicide?
Giovanni's actions and backgrounds were much more melodramatic and realistic than (for lets say...) Cyrus (Who wanted to make a new universe without soul). Team Rocket committed actual crimes like burglary, Pokemon slaughter, hostage standoffs, and kidnappings.
Other Alternate Theories Thought Up
1. Giovanni used Waterfall to get out of Tohjo Falls, thats why there was a splash noise.
Reason to disagree: None of Giovanni's Pokemon are capable of using Waterfall, and to get to his hideout, you go through the Kanto entrance. Which has no need for the Waterfall HM.
2. Giovanni dived and swam out.
Reason to disagree: Sharp rocks! High cliffs! Deadly!
3. Gone to a secret island to enjoy his life with John Lennon, Jimmy Hendrix, 2Pac, and Michael Jackson.
Reason to AGREE: OHHH YAAA