The Emperor had very limited actual power. Officially he was the head of all Japan and the superior of the shogun, but in practice he spent his time performing calligraphy or other various arts while the Shogun conducted business. That being said, the Shogun, and later, those who controlled the Shogun (Nobunaga and Hideyoshi, specifically) issued commands in the Emperor's name. One notable instance of the latter was when after a five year siege against the great monk fortress of Ishiyama Honganji, Nobunaga finally sent a letter that he had orchestrated with the Emperor asking the monks to surrender, and the abbot agreed.

There's an interesting account from the Portuguese Jesuits in this time period, who felt that if they could just get an audience in front of this emperor fellow, they'd win converts all over Japan.

What they found was a Kyoto that was basically run down and powerless. The Emperor had no say in anything important, and reputedly had to sell his calligraphy in the street to make ends meet.

They realized that the warlords had all the power, and did a pretty good job forming an alliance with Oda Nobunaga. Oda probably didn't convert, but many of his relatives and members of his court did, he liked Western technology, and he thought the Jesuits were a lot better than Buddhist priests, due to the Jesuits rather severe lifestyle.

If Oda hadn't been assassinated, the course of Christianity in Japan would have been very different.