What is the censored line in this prayer? Why was is censored and what does it mean?

Hi,
Thanks for asking this question.
The following is an excerpt taken from the Artscroll Siddur. It is probably the best prayer book out there today with amazing commentary and references.

You can find this information on page 159 of this book. Also, the aleinu prayer was originally written by Joshua, the man who took over the reign of the Jewish people after Moses. It has tremendous holiness and should not be taken lightly.

The line you are referring to is translated as “For they bow to vanity and emptiness and pray to a G-d which helps not.” (Isaiah 45:20)

This is the commentary:
For they bow… The inclusion of this verse follows the original version of this prayer. In the year 1400, a baptized Jew, no doubt seeking to prove his loyalty to the church, spread the slander that this passage was meant to slur Christianity. He ‘proved’ his contention by the coincidence that the numerical value of the Hebrew word used above meaning ‘emptiness’ is 316, the same as yeshu, the Hebrew name for the Christian messiah. The charge was refuted time and time again, particularly by Menasseh ben Israel, the 17th century scholar, but repeated persecutions and church insistence, backed by governmental enforcement, caused the line to be dropped from most ashkenazik prayer books. While most congregations have not returned it to the aleinu prayer, some prominent authorities, among them Rabbi Yehoshua Leib Diskin, insist that the aleinu be recited in its original form. (This was taken from World of Prayer, Siach Yitzchak)

I hope this answers your question.
Be Well,
Rabbi Litt