The Shogunate was a massive, advanced mech that was created by the Japanese Polity to surpass the gen:LOCK program. It was also supposed to defend Japan from invading Union forces.
Unlike the Holons that are piloted only by one mind, the Shogunate is piloted by over two thousand minds according to Genji Anno.
At the end of gen:LOCK issue #9, and in issue #10, Sycorax, with Julian temporarily in its control, hijacks the Shogunate and attacks Osaka. Ultimately, it was destroyed by the gen:LOCK team with help from both Japan under Anno and the Union under Carlyle through orders of Yasamin Madrani.