According to the anime, Ho-Oh lived in the Tin Tower in ancient times. When a war broke out, burning both the Tin Tower and the Brass Tower down, it created Raikou, Entei, and Suicune, and all four disappeared. Later, a new Tin Tower was erected, but Ho-Oh since then has never come back for sure. A sacred flame known as the "Prayer Flame" from Ho-Oh burns in the Dragon's Den; it was obtained during the same war.
Ho-Oh was seen flying into the sunset at the end of Battling the Enemy Within!. This time, Brock, May, Max, Scott and Brandon saw Ho-Oh as well (on a slightly related note, this time, someone other than Ash managed to identify it first).
Ho-Oh had a cameo appearance during the opening sequence for Jirachi: Wish Maker.