After every episode of The Intruder, a password was given that could be used to unlock a Flash game on Toonami.com. The games involved the player leading the "Clyde50-B" robot around and saving Clydes from the Intruder.
TOM and SARA are having a regular conversation in the control room when something shakes the Absolution. Investigating, TOM notices a hole in the right engine, at which he is perplexed as to the cause. Since SARA cannot give any conclusive data, TOM patches the hole with a sheet of metal, unaware a red blob is slowly moving below. Back on deck TOM is informed that there is an intruder in the engine, but SARA cannot detect what it is. TOM goes to investigate with a loaded weapon, but is knocked into space by the red blob. SARA sends some drones to retrieve TOM as he reactivates. Requesting a jet pack, TOM soon returns to the ship's bridge to learn that the intruder is on three different decks at the same time. TOM sends drones down to investigate and is able to distinguish that the ship is still being consumed by the intruder before the drones themselves are eaten. TOM then heads down once again with a charged rifle to take down the intruder. However, he is unsuccessful in incapacitating it, and he himself is eaten by it. Afterwards, SARA begins downloading his memories and personality and such into a taller, sleeker and darker 2.0 version of TOM as the Intruder continues to consume the engine. When TOM wakes up, SARA tells TOM that the only way that the Absolution is to be saved is by using explosives to remove the starboard engine from the ship. TOM is successful, and sends the engine and the intruder off into the depths of space. Shortly afterwards, TOM is seen calling for a replacement for the engine that they lost to find that it is no longer in production. Instead, he is given a choice of three different engines, thereby giving the opportunity for the audience to choose. Arriving a month later at the repair station, TOM orders the Talon S.T.s as chosen by the audience. As the absolution leaves, the intruder can be seen floating in space, with the final caption "End?"