The first, second and ninth KUNOICHI competitions had no traditional Third Stage, as there were only three stages, making the original 3rd stage the Final Stage. The third tournament introduced a regular Third Stage, which, unlike the SASUKE counterpart, had a time limit, which no SASUKE competition with the exception of the 29th has ever had. KUNOICHI 5 abandoned the full-stage time limit, reserving it as part of the final obstacle, and the next tournament removed the time limit altogether. The eighth tournament replaced the traditional format of the Third Stage, instead introducing a competitive, single obstacle challenge known as the Flying Roll, similar in design to the Monster Box.
The ninth tournament once again only used three stages in similar fashion to the first two competitions, only for the traditional Third Stage format to return in the tenth tournament, renamed as the Black Stage to keep in pattern with the ninth tournament's color-based naming for its stages, with the exception of the Final Stage. The tournament would have five obstacles featured in the stage, the most in a single Third Stage in KUNOICHI history. This redesign brought most similarities to the SASUKE version, as while previous competitions mainly relied on extreme balance-based obstacles, the new Third Stage featured obstacles mainly meant to test the upper body-strength of the competitors.