it could be....

Mitsume ga Tooru, a Japanese game that I hear means something like "The Three Eyed One" I don't read Japanese so I have to go on what other websites tell me.

Mitsume ga Tooru is also available in Vimm's Lair, both in Japanese and with the English translation.

Here are some other links though:
Rescue - The Embassy Mission (U).nes

Mitsume ga Tooru (J) [o1][T+Eng1.01_Toma].nes

Mitsume ga Tooru (J).nes

I can't find any info on 3 eye story but Resuce - The Embassy Mission is available to download here at Vimm's Lair.