When you first load the beta, let it run for a few seconds and some Japanese kanji will appear explaining what the story is. Thanks to Anton Berglin, we now know what this means in English:

Ninja... they are an indispensable shadow for secretly retrieving
information or defense.

Moreover, the world of ninjas has in every epoch been divided in two
forces. One is a wicked clan bent on ruling the world by
means of dark power. The other is the good Oboro clan, restraining the
evil clan and preserving the peace equilibrium.







Neo Zeed. Threatening the world in the past, it was thought that this
gigantic crime organization been crushed completely at the hands of
the exceptionally gifted Joe Musashi from the Oboro clan. However,
"Masked Ninja" -  the leader of Neo Zeed -  who had been defeated two
years earlier, was only the puppet of the true leader "Shadow Master".






And so, with Shadow Master as it's origin, Neo Zeed was reborn, taking
the new name "Neo Ghost", and restarting it's activities.

And in order to get rid of the nuisance Joe Musashi, they started to
extend their evil influence to Ninja Village*.


*(It's not "the ninja village", or "the ninjas' home" even though that would
seem more natural, it's written as if it's the name of something.)

Check this video to see the intro in motion, note how there is no sound or anything played during it. The whole Neo Ghost deal was dropped from the final game, the bad guys kept their name of Neo Zeed instead. Also, "Masked Ninja" was the final boss of the original Shinobi arcade game -"The Boss" was the name of the final boss from The Revenge of Shinobi, and he was meant to be the Neo Zeed leader, so it looks like SEGA got a little confused with their bosses there.