In Phantasy Star II, you revive dead characters by cloning them. This means that by the end of the game, the original characters are likely to all be dead and replaced by clones (and some of those clones have probably been replaced by other clones).
This is actually touched upon in Phantasy Star Online 3 C.A.R.D. Revolution when a woman accidentally gets the man she loves killed while trying to get his attention and has to deal with seeing him return with no memories from after his last physical/secret memory backup appointment.
It gets worse in the Japanese version; everyone gets cloned after Gaira's destruction.
In the finale of the game Rolf and his party are forced to destroy Mother Brain in order to rid the influence of the Dark Force over Algol. While this is noble, the fact of the matter is that for the past 1,000 years Mother Brain had been essentially taking care of the Palmans. When Mother Brain was destroyed, you had an entire population of Algol who had no idea how to take care of themselves. In Phantasy Star IV, it's revealed what followed the destruction of Mother Brain was a catastrophe known as "The Great Collapse", where ninety percent of the population of Algol died.
However, note that this isn't really a case of Nice Job Breaking It, Hero, since the computer was already nuts. Your party just makes the disaster natural rather than artificial.