The eight levels on offer in this beta are almost all completely different to the ones found in the final game, with only a few ideas kept from this version to the version released. Also, unlike the final version, none of the levels have proper names.
Joe starts his quest in a dark forest, which is populated by many ninjas along with machine gun-totting and grenade tossing soldiers. A little bit later though the entire place catches fire and Joe has to take on more enemy soldiers. The burning forest idea was actually kept for the final game -it is used in the fifth level.
The second level takes place outside a Neo Ghost base which is guarded by several fatties with extendo-arms, who never made it into the final game. Inside the base there are more oddities, such as tigers and flying robots, along with a boss who isn't as friendly as your average E.T.
Starting off in the sewers, the first few sections didn't make it to the final game, but near the end of the level there are a couple of areas that would eventually be used, albeit with several changes. The boss for this level is also used in the final game, although his colour was changed to brown instead of red.
This is where the level order differs from the final version, as instead of taking place at the sea like in the final version, this level is all on land and is mostly indoors.
Starting out at what appears to be outside a Neo Ghost base, Joe will eventually reach an oil refinery which is guarded by a Terminator style robot with a big gatling gun.
Whilst the previous two levels weren't really incorporated into the final game, this one was as it features the factory were an army of robot Godzilla type monsters are being made. This stage is also the shortest in the beta.
This level looks like it was completely dropped from the final game, it is all outdoors and is also the biggest level in this beta. It may have eventually been turned into the ninja house (level 6) of the final game, and it also features "The Boss" -the final enemy from The Revenge of Shinobi.
Whilst the last level of the final game took place on Shadow Master's sky fortress, this level takes place inside Neo Ghost's big base which certainly isn't up in the sky. The final boss is still Shadow Master though, but like any of the other bosses he can't attack you and vice versa.