Actually, GT is non-cannon, since Akira Toriyama wasn't the one who wrote the story, he only did the SSJ4 design.
A lot can be said about the last episode.
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You could argue that Goku went to train with Shenlon, you could argue that he offered his own life for that last wish, you could argue that it was all an illusion, seeing Pan holding his shirt after he had supposedly left, you could argue that he became one with the Dragon Balls/Shenlon, you could argue that he"d become immortal.
This list goes on and it will remain to your own imagination what you believe has happened to Goku, as it was never thoroughly explained in the smashville247.net. I guess if anything, we could agree that Goku had surpassed human existence and entered a state different from being alive or dead as we know them.
Goku was dead to begin with at the end of DB GT, and when asked if they should revive him back, he didn"t let them do that. Instead, he feared that there are more dangerous and strong fighters in the world, and he needed to practice and therefore went with Shenron to practice and live a peaceful life for sometimes.
He did mention he will come back when the time is right, and since then there were rumours that a new season will come. But at the moment, there isn"t any and GT weren"t part of the original Dragon Ball series.
Dragon Ball GT is an alternate timeline.
After Super or maybe later in the series, they might reintroduce Super Saiyan 4 as the "Lost Form" or the "Forgotten Form" or something like that.
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My other theory is that maybe the people who created Dragon Ball will create a story where GT Goku and DBS Goku will eventually meet up... when the time is right.
I think that when GOKU went with shenron and meet his old friends for farewell he know that his time has come to say goodbye .And when goku said to shenron that he was feeling very tired than ever before it"s because he was dying and disappears .Also the reason pan saw goku"s dress in the end because he was dead