My fiancé is a missionary here in the U.S. he has however overextended his stay here, we have been together for 1 year we would like to get married. I am a Naturalized American Citizen since the age of 10 when I was adopted by Americans. My only concerned is that in order for me to grant him citizenship he will need to go back to His native country. Please Advise.

You don't grant him anything... they have to apply for a green card and receive it... then they have to meet all the requirement for a number of years before they even qualify for naturalization.

And marriage is NOT a shortcut...

I understand that.
And I am not in anyway, trying to take a shortcut.

Maybe I worded myself wrong, but my only concern is that he will need to go back to his country for the this process?
I have heard that before but I thought it was only if they entered the US ilegally. He entered the country legally with a visa.
We plan to travel around the world, doing missions.. But I'd like to settle down here in the U.S.
Do you think he will need to go back.

If you follow the rules they will see he is here illegally and reject his application. And tell him to reapply from his home country. After all he doesn't have any current papers that show he is here legally RIGHT NOW.

You must get married to apply for his permanent residence (green card). As he is currently out of status, he is subject to deportation.

After you are married, he can leave to apply for the immigrant visa in his home country or stay here and you file the I-130 relative petition and concurrently file the I-485, application for permanent residence, the I-765 for an EAD and all other supporting forms. You will be filing under INA section 245(a). This section of the immigration act allows for a waiver of his visa overstay if he is an immediate relative (spouse of USC).

He will be scheduled for biometrics and then for the interview at the USCIS Field Office. It is taking about 4-5 months for interviews to be scheduled at most of the higher volume field offices and "super districts".

If approved, he will be granted conditional permanent residence, valid for 2 years. He will need to file form I-751 to remove the conditions within 90-days of the 2 year mark. At that time, his PR card will be re-issued and valid for 10 years.

If you are still married, at 2 years 9 months, if he meets the 3 time requirements, he can file for naturalization to become a USC.

I would advise consulting with an immigration attorney, as there may be issues of "preconceived intent" on entry if he came to the US with a B-2 or R-1 visa and the bona fides of the marriage, etc. congratulations and good luck.