When the creator of the original two Box robots went mad, his friend Madison Jeffries had no choice but to use his mutant abilities to take over the robotic form. He then used his metal manipulating abilities to re-shape the previous version into a new, more malleable version of box. 
As the newest incarnation of Box, Jeffries was able to use his powers to make this version of the Box robot into “Swiss army knife” of armor; creating whatever tools he needed, whether it was weaponry or becoming a vehicle.
While Jeffries did maintain a fairly consistent “look” to his robot, he would occasionally change the appearance and colour scheme.
Durability: Model 2 was composed primarily of a “living metal” (the exact details of which were never disclosed) and demonstrated superhuman durability (e.g. able to resist deep sea pressure).
Shape-shifting: Jeffries can use his psionic powers to create new technologies and adaptive equipment for Box, or to modify existing devices within Box and alter its shape, in any way that he can conceive. For example, he has caused part of Box's body to become a cannon and a weapon capable of discharging living light. When Box flies, he can cause its arms to become wings or extend them from his back and a rudder to appear on its feet. He has also caused a drill to emerge from Box's feet and has created weaponry adapted to face whatever foe is being confronted. Jeffries is able to alter the robot as needed such as forming weapons or adapting sensors, in addition by drawing upon outside material, he can increase the size of the robot to unknown limits.
Flight: The Model 2 was equipped with boot jets and stabilizers allowing it to fly with speeds up to Mach 2 to orbital velocity. Jeffries’ version was able to make use of and expand those abilities with the ability to generate wings or larger thrusters.
Weaponry: This version was cable of directed energy blasts from its palms. The exact details are not known.
Sensors: Model 2 had a wide array of sensing and tracking capabilities, including the ability to interface with computers and intercept radio signals.
Operation: Unlike the previous version, this model allowed users to “phase in” and actually become one with the robot. There was a danger in remaining part of the robot for too long and forming a permanent symbiosis and not be able to “phase out.”
Strength: The “standard” Box robot form possessed superhuman strength, able to lift/press 85 tons. Jeffries can cause the Box robot to grow to enormous size, thereby increasing its strength. The uppermost limit of Box's strength is unknown.