Cobra is captured easily (they surrender) by GI Joe at their Lapland Base and taken to Alcatraz Prison (recommissioned as a prison once again exclusively for captured Cobra troops). Cobra Commander reveals on the boat ride (in full Cobra uniforms and Metalhead retains possession of his backpack-mounted missiles) to the island jail that this is a scheme to steal the new Comstock Load submarine which has a shipyard very close to Alcatraz. When the Cobra troops arrive on the island they are issued prison uniforms (but Cobra Commander retains ownership of his metal helmet, Destro retains possession of his gold helmet, Metalhead retains his communication eyepiece and curiously all Cobra characters retain their Cobra uniforms under their prison garb in direct violation of obvious weapons & armor rules in prison). There is a subplot about the "Ghost of Alcatraz" to enable Metalhead to play up his comedic relief Norville "Shaggy" Rogers imitations. (GH-G-GHOST!)
In the kitchen Cobra Commander contacts the Baroness through Metalhead's communication eyepiece to attack the island prison. There is a short pie fight at the "RAW DOG PIE SHOP" (?!?) in which Cobra Troops and the Baroness are stealing pies (?!?) but is used to establish the plot point that the informant noted at the beginning of the episode was a Cobra agent in disguise. Alcatraz Prison is then attacked, taken over, Destro uses a voice modifying device to impersonate Pathfinder's voice to delay GI Joe's retaking of the island. Pathfinder is jailed with the female Warden while Metalhead does more Shaggy impersonations. There are some land-based battles with tanks to obtain control of the Comstock Load submarine (which is rather silly tactically as controlling an island base is only valuable for sea or air attack given that boating in tanks is more cost efficient tactically to drop at the attack point and not an island THEN later a shipbuilding dock). Granted there is a water-based attack later, but it is all tactically inane. Cobra Commander and the Baroness steal the submarine to reveal that the secret weapon was a "PM Generator" (EMP - electromagnetic pulse) that protects the submarine and disables weaponry at a radius of 5 miles.
The reason this episode is problematic is that the forced comedy and often less creative "World Domination Schemes". Stealing a submarine with a defense barrier is a workable tactical move (force the enemy to destroy their own military might), but not much of a World Domination game. Capturing a prison is workable, but usually to gain reinforcements or free a prized ally. The main rule of ground combat is that it can be easy to capture a land, but is often very expensive to hold a captured zone (you have to leave troops & weaponry vulnerable while tactically those troops could be used to eliminate enemy troops). Most of these DIC GI Joe episodes seem to be irksome filler material, chatter, barely comedic "BOINK!" sound effects, and time-wasting. Very little involves tactical maneuvers or serious World Domination Schemes. The GI Joe troops seem a tad more realistic (bumbling, thoughtless, easily captured), but only because Cobra has been neutered to a less threatening status.