The most notable design feature of the Megadoomer is its ability to become invisible; however, it appears as though the mech was never properly tested before it was to be shipped to Tenn, because the Almighty Tallest probably wouldn't have sent it to her had they known its crippling, painfully ironic flaw: while cloaked, the Megadoomer itself remains entirely transparent, yet its pilot sits completely visible. This is likely an intentional flaw by its creators, the Vortians, to weaken the Irken army.
The Megadoomer is colored in the dark reds and greys not uncommon to other Irken vehicles, and sports the "one-eyed" Irken symbol on its hull. It also walks on what GIR pointed out to be "chicken legs". It appears to have no conventional windows, and is piloted manually. Purple's only reaction to the Megadoomer was that he "didn't like it."
The Megadoomer is heavily armed, and its armaments include numerous artillery cannons as well as an excessively powerful weapon known only as the "Doom Cannon." Zim was seen repeatedly pressing this as the ship remained invisible.
As mentioned previously, when the Megadoomer's cloaking device is activated, the vehicle itself is turned invisible but the pilot is not, effectively rendering the entire cloaking system useless. Objects such as bushes and other debris getting stuck on the Megadoomer will also appear visible, making it more easily trackable by the enemy.
An interesting note brought up in the commentary for the Megadoomer episode is that when Zim was in the Megadoomer's cockpit, he was lit by the cockpit's red lights and is colored red accordingly. However, when the mech turned invisible, Zim was colored in conventional night-time lighting. This discrepancy was refuted by the claim that the red lighting of the cockpit too becomes invisible, leaving Zim to be lit by what lights there are outside the vehicle. Oddly enough, Zim himself could still see the interior of the cockpit, even while in stealth mode.
The Megadoomer is equipped with self-destruct capability, presumably to destroy it if it were to be in danger of being captured by an enemy (or in the episode, photographed by Dib). The Megadoomer also ejects the pilot out of the rear of the ship and sends an automated message to the Massive after it self-destructs, informing the Tallest of its destruction.
Throughout the episode the Megadoomer appeared in, power supply problems present themselves constantly. When Zim and GIR unpacked the mech, they found that batteries weren't included, forcing them to plug a massive power cable into conventional Earth power outlets to sustain the mech's power draw. Though this solution allowed for Zim's resultant impulsive rampage in the Megadoomer to continue, it proved to be far less practical than the batteries (which would have allowed the mech to remain self-contained, at least for some time) would have been; Every time the Megadoomer moved too far from the power outlet it relies on, Zim had to summon GIR to locate another outlet closer to the mech.
This problem continued when Zim prepared the (unseen) Doom Cannon to kill Dib: the cannon required so much energy to charge that it shut down the entire city's electricity, and ended up never even being used.