Mega Zygarde's body undergoes a dramatic transformation. Notably, it loses most of its body armor except for chest armor and an armored, crowned head to resemble a more humanoid and less dragon-like build. Its main body features a striking combination of dark and light green colors. Underneath the chest armor, there is a three-hexagon pattern, with two hexagons located on each of its legs. The legs and feet have a rhomboid shape topped with two triangular shapes. Additionally, each leg has two black hexagons and one white hexagon attached to its center. The arms resemble a two-fingered hexagonal hand. Mega Zygarde's tail connects to the chest armor like a cape, while the chest armor itself resembles tree roots. At the center of the chest armor, there are two long hexagonal shapes with three longer ones positioned to the sides. The chest armor features red and blue hexagons, each surrounded by three green hexagons. Mega Zygarde's head is adorned with a green headpiece shaped like flames. Its eyes are green as well, and the lower part of its eyes connects to the pink part of its chest armor. Only two black hexagons of Mega Zygarde remain, connected to two black squares at the bottom of the well. Surrounding the head is three-spiked neck armor at the front, which connects to two long black spikes and one triangular black spike behind the head.

Mega Zygarde's most distinguishing feature is the giant, hammer-shaped cannon attached to its six 90-degree arms on its chest armor. The cannon has a cylindrical shape, decorated with several rectangular shapes and lines. The cannon resembles a tree trunk. At the center of the cannon, there is a pink symbol resembling a cross between an "X" and a "Y" surrounded by red, blue, and pink lines. The middle of the cannon has three long, dark red and dark blue pentagon-shaped elements at the top and three pentagons on the bottom of the cannon, respectively. Next to the longer upper rectangular shapes are a light red and a light blue hexagon. Six rectangular shapes are attached to the back of the cannon. The interior of the cannon features a circle, three hexagons, and a central circle. The back of the cannon has a dark green hexagon at the center.

Mega Zygarde was first discovered in Lumiose City. This form of Zygarde was said to be born from the people's emotions during an unexpected crisis. In response, Mega Zygarde emerges to calm the situation with its unmatched power. When it attacks with its cannon, it maneuvers it using its six arms. The cannon then opens up in the shape of an "X", a "Y", then a "Z", and unleashes a pink light blast that defies all laws of nature. The cannon's blast was powerful enough to destroy a powered-up Light of Ruin attack launched by Hyperrogue Ange Floette, which threatened to annihilate all of Lumiose City. L notes that Mega Zygarde's unique attack resembles the Z-Moves found in the Alola Region Additionally, the cannon activates when Mega Zygarde executes specific attacks while not firing simultaneously.