Wiki says it's the second official prequel to Blame!
Biomega is providing the reasons the Megastructure was created in the first place. It's thousands of years before NoiSE and thousands more before Blame! begins, so Toha is the only recognizable faction. By the time of NoiSE, more recognizable features like the NetSphere, Safeguard and Silicon Life exist, but the world still hasn't gone totally pear-shaped yet (though it takes place right at the point that NTG were rendered the only means to access the NetSphere).