In Him. Forget what "some" do. The Holy Spirit witnesses to you. He won't tell you one thing, and then someone else something different. HE is the interpreter and applier.
So there's this guy, Bob, who while reading Scripture is convinced the Holy Spirit is telling him that Scripture says and means X.
There's this other guy, Greg, who while reading Scripture is convinced the Holy Spirit is telling him that Scripture says and means Y.
Both claim to be submitting to the Holy Spirit and that it is the Holy Spirit leading them to their understanding of Scripture.
Obviously Bob and Greg can't both be right.
And, indeed, Bob says Greg is wrong because Greg is not listening to the Holy Spirit but is instead listening to human wisdom and tradition.
Conversely, Greg says Bob is wrong because Bob is not listening to the Holy Spirit but is instead listening to human wisdom and tradition.
See why there might be a problem here?
The problem here, ultimately, is that both Bob and Greg are claiming to have direct, special insight to the Scriptures through direct, special illumination from God via the Holy Spirit. Neither are willing to admit that they are only fallible human beings, and fallible human beings have not been promised by God special, direct spiritual illumination of Scripture; and so both have placed themselves in the position of being their own super-pope.
Why "super-pope"? Because even the Pope in Rome does not consider all his views as the infallible illumination of the Holy Spirit, and is always held accountable to the wider interpretation and authority of the Church. In other words, if the Pope were to claim to speak infallibly on a subject that is completely antithetical to the core tenets of Roman Catholic Christianity the Pope would be regarded as a heretic.
Egopapism--the idea that one is one's own pope--is what many well-meaning Christians are ultimately subscribing to. They are electing themselves as their own pope, their own supreme religious head, by speaking and thinking that they have a special access to Scripture and that God speaks specially to them. They are unwilling to accept their own fallibility, but speak as though God Himself illuminates and enlightens their minds to the right understanding of Scripture. If one wants to know "Why so many denominations?" This is certainly a significant reason why.
Scripture certainly never promises this. Indeed what Christ said the Holy Spirit would lead "you" into all truth He was not talking to you or me or the Pope in Rome, He was talking to His twelve apostles; further the "you" here is plural, not singular. No individual is promised to have "all truth". Why would I consider this interpretation to be more valid than that interpretation that individuals are led to "all truth"? Here are a few reasons:
1) The grammar: The Greek word ὑμᾶς is the accusative
plural substantive form of σύ ("you"). Modern English lacks a plural second person pronoun, except colloquially (e.g. "y'all"); though "you" used to be the plural and "thou" the singular; thus such nuances can be lost in modern English translation.
2) The occasion and context of the text: We need to go back several chapters to John ch. 13, as this begins following the Supper while in the company of His apostles, to whom He is speaking directly.
3) Christ established a gathered community: In Matthew ch. 16 Jesus, talking to Simon Peter, says, "You are Peter, and upon this rock I shall build My Church." The Greek word translated as "Church" here is ἐκκλησία, meaning roughly "a called out gathering". In the ancient democracy of Athens all free men would be summoned to a place outside the city to gather for voting, this gathering outside the city was the Athenian ἐκκλησία. It is a gathering, a community of people that Christ calls and establishes. Jesus did not institute a "Me and my Bible" study guide to be done alone in a corner; He instituted a Church and called apostles to go and build that Church by preaching the Word He gave them, which they did, and communities of Christian people sprouted up from as distant places as Jerusalem and Rome. They didn't have a Bible to read, but they had a community of faith to participate in.
-CryptoLutheran