Kyoko is a third-generation Royal Tree partnered with Noike, but is of a special and secret design that came about after the attack by Ryoko 700 years prior. During that attack, many of the third generation Royal Trees proved to be of no match for Ryoko and Ryo-Ohki. However, Trees like Yosho's Funaho-fune and Ayeka's Ryu-Oh, who were second-generation Trees, proved to be more of a match. Therefore, Kyoko was specially-modified to be as powerful as a second-generation Tree. Because of this, Kyoko is a state secret, second only to Tenchi. As a result, Kyoko doesn't get many visitors, and can get lonely at times.
Whenever Noike is inside Kyoko, she can interact with the tree by means of an autonomous control unit, which looks similar to a Masu. However, because Kyoko is so lonely, the control unit will often become an attention hog whenever talk is not of Kyoko, as evident when Tenchi came onboard Kyoko by invitation of Noike for lunch.[1]
In the fifth season, it is revealed that Washu has "tuned" Kyoko's Masu interface and, as a result, she is on par with a First Generation Treeship.[2]