For the most part, the Gray Zeta has similar appearance as the standard Zeta, save for two differences: the tail binder, instead of lying down on the back in Mobile Suit mode, instead splits into two horizontal airfoils behind the head; and the thrusters on the lower leg have three small exhausts in place of the standard two.
Weapon wise, it has a new wider shield that covers a greater portion of the unit's underside in Waverider mode, and has two built-in, rapid-fire beam machine guns. The shield also no longer serves as the unit's nose - instead, a large beam launcher is mounted in its place, which detaches and is hand-carried in Mobile Suit mode.
The Gray Zeta has the same beam-deflection coating as the MSN-00100 Hyaku Shiki, which gives it its yellow color (much to the chagrin of its pilot, who wanted it to be a gray color). It is fitted with the split-panel cockpit screen of old MS like the Zaku rather than a modern panoramic monitor.
After the Gryps Conflict, three Zeta Gundam was made and assigned to AEUG for wiping out Titans remnants. The Zeta Gundam 3B Type was piloted by Shin Matsunaga (Gray Wolf), a Newtype and former Zeon's Ace. Together with Amuro Ray's MSZ-006-3A Zeta Gundam 3A Type and Yurii Ajissah's MSZ-006-P2/3C Zeta Gundam P2/3C Type, Shin confronted the monstrous mobile armor, QRX-006 Geminus. During the battle, Gray Wolf crashed his Zeta into the enemy unit in an attempt to expose the enemy's movement patterns to his allies.