Quick Kick, Alpine, and Bazooka escape the Cobra cargo plane on Trubble Bubbles and commandeer a Cobra helicopter to return to Joe Headquarters. As the Crimson Twins broadcast their threats, Shipwreck and Snake-Eyes arrive at Headquarters with the laser disc of the cubes' schematics. The Joes on Space Station Delta retake control from the Dreadnoks and shut down the Pyramid of Darkness, allowing the Joes at Headquarters to access the laser disc and communicate with the other Joe teams. Cobra Commander regains command of Cobra and orders the pyramid reasserted from ground level, but the effect is only intermittent.
Quick Kick's helicopter crashes into Joe Headquarters, and his knowledge of Cobra's location allows the Joes to mount an assault and ultimately destroy the cubes from the base. Cobra Commander and the Crimson Twins flee to Enterprise Towers, which they convert into an armed rocket. Satin reappears and helps Shipwreck and Snake Eyes stow aboard the rocket and fight long enough for the Joes on the space station to rig a proton beam to destroy it. The Joes escape the rocket on Trubble Bubbles, and the Cobras on the rocket and space station return to earth in escape pods (with the Dreadnoks in a garbage module). The Joes celebrate as Cobra once again goes underground, blaming one another for their failure.
| Featured Characters
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| Cobra Commander | 246 seconds | 27 lines | retaking command, fleeing to battle rocket; disguised as bag lady
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| Shipwreck | 195 seconds | 22 lines | returning to Joe HQ, in V.A.M.P. II attacking Cobra base, escaping battle rocket in Flight Pod
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| Tomax | 181 seconds | 19 lines | at Cobra base, flying Rattler to Enterprise Towers/battle rocket, escaping by subway
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| Xamot | 178 seconds | 19 lines | at Cobra base, flying Rattler to Enterprise Towers/battle rocket, escaping by subway
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| Quick Kick | 122 seconds | 13 lines | returning to Joe HQ, attacking Cobra base, yodeling to bring down Dragon
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| Snake Eyes | 116 seconds | | returning to Joe HQ, in V.A.M.P. II attacking Cobra base, escaping battle rocket in Flight Pod
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| Gung-Ho | 107 seconds | 11 lines | in charge at Joe HQ, in Silver Mirage attacking Cobra base
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| Alpine | 104 seconds | 12 lines | returning to Joe HQ, attacking Cobra base, yodeling to bring down Dragon
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| Bazooka | 91 seconds | 3 lines | returning to Joe HQ, attacking Cobra base, yodeling to bring down Dragon
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| Torch | 83 seconds | 10 lines | captured on Space Station, freed by Zartan, escaping in garbage module
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| Ace | 73 seconds | 2 lines | at Joe HQ when Shipwreck returns, part of attack on Cobra base
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| Polly | 71 seconds | 3 lines | returning to Joe HQ, with Shipwreck attacking Cobra base and battle rocket
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| Ripper | 60 seconds | 2 lines | captured on Space Station, freed by Zartan, escaping in garbage module
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| Wild Bill | 59 seconds | 3 lines | at Joe HQ, attacking Cobra base
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| Destro | 57 seconds | 6 lines | kissing the Baroness; supporting Pyramid of Darkness; disguised as construction worker
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| Baroness | 56 seconds | 3 lines | kissing Destro; supporting Pyramid of Darkness; disguised as a nurse
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| Zartan | 56 seconds | 3 lines | held captive by Dreadnoks and then by Joes, fleeing in escape pod
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| Buzzer | 54 seconds | 3 lines | captured on Space Station, freed by Zartan, escaping in garbage module
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| Mutt | 52 seconds | 4 lines | helping retake Space Station Delta
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| Dusty | 42 seconds | 3 lines | helping retake Space Station Delta, freeing Duke, rigging proton beam
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| Flint | 34 seconds | 9 lines | communicating with Joe HQ from U.S.S. Flagg, flying Skystriker over Enterprise City
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| Duke | 16 seconds | 2 lines | freed on space station, rigging and firing proton beam
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| Junkyard | 15 seconds | | retrieving Fatal Fluffies' whistle to help retake space station
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| Lady Jaye | 14 seconds | 4 lines | on U.S.S. Flagg, flying Skystriker over Enterprise City
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| Background Characters
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| Stalker | 34 seconds | 1 line | at Joe HQ, attacking Cobra base
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| Cover Girl | 34 seconds | (silent) | at Joe HQ when Shipwreck returns, part of attack on Cobra base
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| Spirit | 31 seconds | (silent) | at Joe HQ, attacking Cobra base, erroneously seen on space station
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| Roadblock | 28 seconds | 1 line | attacking Cobra base
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| Timber | 25 seconds | | returning to Joe HQ, with Shipwreck attacking Cobra battle rocket
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| Tripwire | 19 seconds | (silent) | at Joe HQ, attacking Cobra base
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| Steeler | 18 seconds | (silent) | helping retake Space Station Delta, erroneously seen at Joe HQ
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| Barbecue | 15 seconds | (silent) | at Joe HQ, attacking Cobra base, erroneously seen on space station
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| Clutch | 9 seconds | (silent) | helping retake Space Station Delta
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| Adm. Ledger | 8 seconds | 1 line | on U.S.S. Flagg when pyramid is disrupted and when battle rocket is destroyed
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| Scarlett | 8 seconds | (silent) | helping retake Space Station Delta
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| Breaker | 6 seconds | (silent) | helping retake Space Station Delta
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| Doc | 1 second | (silent) | seen on Space Station Delta (5:25)
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| Troops Appearing
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| Greenshirt | 86 seconds | | at Joe HQ, on U.S.S. Flagg, retaking Space Station Delta, attacking Cobra base
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| Cobra Officer | 31 seconds | 1 line | flying Cobra helicopter, defending Cobra base, covering leaders' escape
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| Crimson Guard | 21 seconds | | standing guard and assembling for battle at Cobra base (twice colored blue)
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| Cobra | 11 seconds | 1 line | parachuting from cargo plane, defending Cobra base, rounded up in last scene
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| Vehicles Appearing
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| Skystriker | 64 seconds | | on U.S.S. Flagg deck, pursuing Rattler over Enterprise City, circling battle rocket
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| Rattler | 59 seconds | | with Destro and Baroness; used to escape Cobra base to Enterprise Towers
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| Trubble Bubble | 44 seconds | | used by Joes to escape cargo plane and later to escape battle rocket
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| V.A.M.P. Mark II | 44 seconds | | used to attack Cobra base and amplify Alpine's yodel
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| Mauler | 13 seconds | | used to attack Cobra base
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| H.I.S.S. | 11 seconds | | used to defend Cobra base
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| U.S.S. Flagg | 10 seconds | | used to communicate with Joe HQ and launch Skystrikers
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| Silver Mirage | 6 seconds | | used to attack Cobra base
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| Slugger | 6 seconds | | used to attack Cobra base
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| V.A.M.P. | 4 seconds | | used to attack Cobra base
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| Bridge Layer | 2 seconds | | used to attack Cobra base (11:19-20)
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| Stinger | 2 seconds | | seen as Cobra base prepares defenses (11:28-29)
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| A.P.C. | 1 second | | used to attack Cobra base (11:53)
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| Non-Toy Characters: Fatal Fluffies, sailors on USS Flagg, Satin
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| Non-Toy Equipment: Cobra cargo plane, Cobra helicopter, Space Station Delta, Destro's wooden vessel, low-altitude pyramid generator, Cobra Dragon, cube hauler, battle rocket, Zartan's escape shuttle
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