The fig tree in Israel is an important symbol, a metaphor expressed physically. We know of Jesus' cursing of the fig tree for not producing fruit.
And when he saw a fig tree in the way, he came to it, and found nothing thereon, but leaves only, and said unto it, Let no fruit grow on thee henceforward for ever. And presently the fig tree withered away. Mt 21:19, (Mk 11:13-20)
Regarding Jesus, the BRANCH, there was a prophecy in Zechariah 3:8-10
Hear now, O Joshua the high priest, thou, and thy fellows that sit before thee: for they are men wondered at: for, behold, I will bring forth my servant the BRANCH. For behold the stone that I have laid before Joshua; upon one stone shall be seven eyes: behold, I will engrave the graving thereof, saith the LORD of hosts, and I will remove the iniquity of that land in one day. In that day, saith the LORD of hosts, shall ye call every man his neighbour under the vine and under the fig tree.
Here is how Jamieson, Fausset & Brown explains the fig metaphor.
- under. . . vine. . . fig tree--emblem of tranquil prosperity ( 1Ki 4:25 ). Type of spiritual peace with God through Christ ( Rom 5:1 ); and of millennial blessedness ( Mic 4:4 ).
Lastly, the name Nathanial means "gift of God". He was the first to say, thou art the Son of God.
Nathanael answered and saith unto him, Rabbi, thou art the Son of God; thou art the King of Israel. John 1:49
So, why was Nathanial under the fig tree?
While it literally happened, he was under the fig tree and Jesus saw him and called him, it was the beginning of the fulfillment of Zechariah's prophesy, of the metaphoric expectation of figs. Jesus' ministry was beginning.