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While the original carrier had served as a mobile headquarters from which Sark enforced the reign of the MCP, CLU plotted a large-scale invasion of the real world using his carrier, the Rectifier. Its purpose was to serve as a mobile fortress to prepare and transport an army through the portal to the real world.
The Rectifier was topped with a docking tower on which Clu's Command Ship landed and attached to. With Kevin Flynn's Identity Disc interfaced to the Command Ship, and that ship then docked to the carrier, it would have potentially enabled the entire carrier to enter the portal and cross over between the two worlds.
The Rectifier contained an immense hangar that ran from bow to stern. The mid and aft sections could hold thousands of assembled personnel along with ranks of Light Fighters and personnel carriers. The long forward section housed numerous Recognizers and rows of Battle Tanks. An open floor on the port side split the deck from the bow to the midsection of the carrier, allowing entry and launch areas for flying craft. This was matched by a shorter port-side gap in the rear of the hangar.
The Rectifier also facilitated the large-scale repurposing of programs for Clu's invasion plan. Solar Sailers would ride in and be docked high in the port side of the hangar. From there, transport modules were detached from the Sailers and lowered to the deck. Programs of all kinds would then exit and be directed to gateways into a revolving "factory" within the huge circular-shaped section on the carrier's mid-starboard side. Rectified en masse, these programs would emerge a short time later, repurposed into Sentry programs.