Art of Fighting 2
Eiji Kisaragi journeyed to Southtown to kill the Sakazaki clan (Ryo, Yuri, Takuma, and I guess Robert counts too, even though he isn't technically a Sakazaki). It seems that the Kisaragi clan has been feuding with the Sakazaki clan for a long time, and Eiji decides to end the rivalry with their deaths. Eiji went to their dojo and found no one there. In his ending in AoF 2, you find out that Eiji likes the ninja girl Mai Shirunai (Andy Bogard's girlfriend). I've heard though, that the Kisaragi clan are also rivals with Mai's clan, so it would be interesting if a relationship developed between them (which is unlikely, seeing as how SNK has pretty much forgotten all about Eiji).
King of Fighters '95
Eiji never found the Sakazaki's in AoF 2, but heard that they were going to enter the King of Fighters tournament. Eiji decided he would enter the tournament to finally face the Sakazakis, but he could only enter if he was on a team. It turned out that Billy Kane, Geese Howard's personal bodyguard, was looking for fighters to join his team in the KoF '95 tournament. Eiji joined Billy's team along with Iori Yagami, a new fighter (Kyo Kusanagi's rival, who would soon become one of SNK's most popular KoF characters). Eiji planned to get rid of his team-mates after the tournament was over, but he never got to. He also never got to get a clean shot at the Sakazakis either. In the end, Iori Yagami used an unknown power (which was probably his Riot of Blood/Orochi mode) to defeat Billy Kane and Eiji Kisaragi. Why he did this is unknown, but he probably knew that Billy and Eiji were going to double-cross him or something (this team was probably the most dysfunctional team in the game, and every member was probably going to get rid of the others if he got the chance). Geese Howard must have found Eiji and Billy after they were almost killed by Iori, because in their ending, Billy says "Hey, you're Geese!" to someone you can't see.
Art of Fighting 3
Okay, Eiji isn't really in this game, but a new ninja character named Jin Fu-Ha is looking for him to take care of some unfinished business (in other words, he wants to kill Eiji). Jin never found Eiji in AoF 3, but he continues his search in his ending (I will try to post it later after I make it into an animated gif). You never get to learn if Jin actually accomplished his goal (I hope not).
Where is he now...?
Currently Eiji's whereabouts are unknown. Some speculate that he is just observing and training to finally get revenge on the Sakazaki's and Iori, but no one knows for sure. Most likely SNK just forgot about him. Okay, SNK hasn't forgotten about him all the way, because he makes cameos in several later KoF games (my favorite is in KoF '98/KoF '99 Dream Match where he helps Billy taunt Iori), and in KoF 2000 he is a Striker for Lin, the Chinese ninja.