Marvel comics continuity
Dirge observes a struggle between G.I. Joe and Cobra for Power Station Alpha from high above and relays it to Shockwave. Due to their common interest in Power Station Alpha, the Decepticons state to Cobra their interest on an alliance. Later, Dr. Mindbender overhears Shockwave informing Bombshell and Dirge of his plan to convert Alpha into a device to tap into the Earth's natural energy...a plan Mindbender realises will destroy the planet.
Shockwave, after getting the Decepticon leadership, shows the Decepticons a video presentation of his plans for the Power Station Alpha. He will use it to extract all conceivable energy from the Earth, and beam said energy to Cybertron, leaving the Earth nothing but a lifeless fireball. At the end of his presentation, Cobra arrives outside their base. The two evil organizations make plans to ally and use Alpha to their mutual benefit, but both are quietly planning to betray the other. Shockwave talks Serpentor into attacking the Autobots at the Ark and retrieving a generator the Decepticons need to make adjustments on Alpha. Dirge goes with Cobra; stays with the Decepticons.
At the Decepticon base, Shockwave instructs Bombshell to dispose of Doctor Mindbender but he is saved by the intervention of the Baroness. The two Cobra agents depart, taking Bombshell with them in insect mode, and depart for Seattle. As the attack of an Autobots/GI Joe/Cobra alliance begins, Shockwave dispatches a group of Decepticon planes to counter the aircraft and also has the Constructicons combine into Devastator. The Decepticons are defeated anyways.
Devil's Due G.I. Joe vs. Transformers continuity
In the absence of the Ark and Nemesis crews, Shockwave had assumed command of the Decepticons on Cybertron, and had successfully driven the Autobots into an underground resistance movement. When a number of G.I. Joe and Cobra troops, along with the captive Starscream, accidentally arrived on Cybertron via an overloaded wormhole gate, Shockwave and his troops immediately surrounded them. The same wormhole malfunction blasted a number of Transformers off of Cybertron and into random points of Earth's past, a temporal anomaly that threatened to scour the Earth's face with fire if the Transformers were not brought back. Ultra Magnus and Perceptor arrived and were able to hold off the Decepticons for a time with a force field, while teams of humans were time-ported away to retrieve the missing Transformers and end the anomaly. Magnus's force field power ran out before all the teams had returned, and Shockwave had his troops capture the Autobots. He took personal pleasure in blasting Ratchet when he was returned through the gate.
Revealing that he had intended all along for the humans to discover the wormhole gate technology, Shockwave set the gate to continue operating but blocked the last remaining group from returning—thus condemning Earth to destruction, easy pickings for conquest.Fortunately for Earth, two members of the G.I. Joe team were able to reactivate the gate, allowing the newly-created Dinobots to return to Cybertron. The Dinobots' power quickly drove Shockwave's Decepticons into retreat.
Regrouping on the other side of the planet, Shockwave had the long-missing Starscream brought before him. As Starscream attempted to explain his way out of being seen as a traitor, a recording of Cobra Commander's voice suddenly began to play, explaining that he had lined Starscream's hull with explosives. Shockwave leapt to try and stop the process, but the entire building exploded, apparently taking the two Decepticons with it.
With Shockwave's defeat, peace returned to Cybertron, and the Decepticons were driven back to a region known as the Gladiator Zone.One of the mish-mash of robot parts known as the "cannibalizers" was seen with Shockwave's blaster hand grafted onto its arm.
As one of the Decepticons who crashed to Earth in the Ark millions of years ago, Shockwave was retrieved by Cobra and pressed into service, taking on the alternate form of a massive artillery cannon. Chafing under the leadership of Cobra Commander, he was ordered to transform and destroy the Autobot Superion. Although he did so, he was forced to fire sixteen consecutive times, despite needing to repair himself after every shot. The resulting strain on his structure irrevocably damaged him, and Cobra Commander refused to allow Megatron to use the power of the Matrix to restore him.