imam james the just

If Islam is true, then what does that mean about early Christian origins? According to the Quran, Jesus (as) is neither God nor the son of God and "they neither killed him nor crucified him" while most Christians generally believe something very different about Christ.

So a natural question would be where the mainstream Christians came from. And where did the original authentic Christians go?

The basic answer which most Muslims give for the first part is to blame Paul. Mainstream Christianity is "Pauline" and largely originates in Paul's distortions of Christian doctrine.

A tricky part is the second question. Can we point to which group or groups form the "real" authentic tradition of Christianity?

I'm not Ismaili, but one of the interesting perspectives I've seen on this question can be found in an article on the Ismaili Gnosis website:  The Imamat of James: Brother of Jesus, Successor of Christ & Leader of Early Christianity The article brings together a couple different ideas I've seen elsewhere. Basically, the author(s) locate the authentic non-Pauline Christian tradition in the Jewish Christian (Ebionite) tradition led by James. It is a really nice round-up of texts arguing for the high status of James in the early Church. For example: 

The disciples said to Jesus, ‘We know you will leave us. Who is going to be our leader then?’ Jesus said to them, ‘No matter where you go, you are to go to James the Just, for whose sake heaven and earth came into being.’

Gospel of Thomas Saying 12

The article also presents evidence outlining the conflict between James and Paul which is there lurking in the Biblical texts, but also in some of the non-canonical writings such as the Clementine literature. Much of this is interpreted by scholars James D. G. Dunn and Robert Eisenman:

“Paul had in effect been disowned by the church which had first commissioned him as a missionary. Since Paul continued to believe passionately in the truth of the gospel which in effect had been rejected at Antioch, the relationship could not continue as before. It is not surprising, then, that in his continuing mission, as we shall see, Paul seems to have worked much more as an independent missionary… It would further follow that Paul saw the outcome as constituting an effective breach with the mother church in Jerusalem.” 

– James D. G. Dunn, Beginning from Jerusalem: Christianity in the Making

I don't think I'd go along with some of the more Ismaili-specific concepts, but these days I'd definitely lean towards some of how they navigate through these controversies.