There are many many many alternative explanations for this. The most commonly accepted are

1) that it was originally meant as a campaign song for acid-guru Dr Timothy Leary when he was going to run for US President (no kidding!), but later John re-wrote it in its present form. Leary's slogan was "come together, join the party", the "come together" alluding to I Ching, the Chinese book of changes.

2) John just liked to write nonsense stuff, it doesn't have any drug meaning or anything else like that. It is a great song, and people should stop criticising the Beatles just because the did drugs. Randomness is the art of tripping. John wrote this song to take the piss. He was probably sick of fans misinterpreting his songs.

3) Each verse is describing one of the four band members.

1: Ringo- the easygoing, level headed one in the group

2:George- the spiritual, naturist, searching for universal knowledge, and freeing your mind(and can wail his monkey fingers on a guitar neck)

3:John- the walrus, life now centered around his wife

4:Paul- the good looking one, having the group's mojo going by keeping them together. It could also have a reference to him "dying", now that it's impossible to see him buried, as he pleads for one, one, and one to "come together over me."

The oddest theory is that the the song is about bukkake, a Japanese term for a sex act where a bunch of guys come on a woman’s face. Allegedly Yoko “exported” it from Japan and turned John onto it. This song is about a particular drug-filled orgy they had, where Yoko ordered: Come together right now over me.

I doubt this very much. Personally I think its a great song, but probably just some cool phrases stuck together

ichi