Meanwhile the war continued and finally the entire energy supply on Cybertron was exhausted. Optimus Prime decides to go on an expedition with his elite forces to find extra reserves. The Decepticons learn from this plan and in this they see the golden opportunity to defeat the Autobots for once and for all. Megatron orders his spaceship to be made ready and also takes all of his elite forces with him. He orders the third robot in command (Shockwave) to stay on Cybertron and guard it till his return.

Just before takeoff from their spaceship; the Ark, the Autobot base is attacked by Decepticons. The Autobots that are selected for this expedition board the Ark during the attack. Elita One hurries to the Ark and begs Optimus Prime to allow her to come with him. Optimus Prime refuses because he doesn't want to expose her to the dangers of this hopeless expedition, but he promises to return for her. Then a grenade explodes between them and as soon as the vapours of the explosion disperse, there is no trace left of Elita One. The Ark departs, just after take off it gets stuck in a meteor shower. Optimus Prime orders the use of the lasers and they plough themselves a way through the meteors. That is the moment Megatron decides to attack, with the lasers empty the Autobots are defenseless. The Decepticon spaceship moves alongside the Ark and the Decepticons board the Ark. a fierce battle follows. The two ships started drifting and get in the gravitational field of a planet and the Ark with all the Transformers on board crashes into a vulcano.

Milions of years later there is a vulcanic eruption. The main computer of the Ark (Teletran One) is reactivated by this eruption and it automatically launches a probe to explore the planet. The probe finds a military jet and sends the data back to Teletran One. Teletran One starts to repair the Transformer that is closest to him and makes that his new transformation is a jet. Unfortunately it was the Decepticon Skywarp that was closest by. Skywarp moves Megatron towards Teletran One and also Megatron is repaired. Very soon afterwards all Decepticons are functional again. They leave the Ark and decide to make a new base elsewhere from where they can drain the energy from this planet and they also need to get in contact with Cybertron, if it even still exists. Starscream gives a blast of his laserriffle as a last salute to the Autobots. This proves to be a very decisive blast, because Optimus Primes body falls over and gets in the beam from Teletran One and he too is repaired.

As all Autobots are repaired, it's their turn to make plans. They also decide there is need to find out whether Cybertron still exists, but first Optimus Prime is interested in this new planet (Earth) that they are on. The Autobots Hound and Cliffjumper go exploring and find the Decepticons. Cliffjumper tries a surprise shot at Megatron, but he misses. Now the Decepticons know that they have the Autobots once again as enemies. A oilplatform proves a important target for the Decepticons, here they make one of their first strikes. The Autobots make a more or less futile attempt to stop the Decepticons on the platform, but they are able to make their first human friends: Sparkplug and Spike Witwicky.

The Decepticons continue their attacks and finally they have all the resources for a spaceship with a full cargo of energon. They manage to depart from Earth, but they have a stowaway; Mirage. Mirage blasts the controls just at the moment that Starscream makes one of his many attempts to overtrow Megatron. The spaceship gets uncontrolable and Mirage jumps out of a door and saves himself with a parachute. The ship crashlands in the ocean.

The Decepticons survive the crash and make a underseas headquarters from their spaceship. Suddenly they receive a message; it's Shockwave. Cybertron still exists, but the energon supplies are now really critical. Shockwave developed a new transport system during Megatrons abscense; a spacebridge. This bridge enables the Decepticons to travel with the speed of light from and to Cybertron.

The Autobots also do a lot of inventions, their most succesfull invention are the Dinobots. These Dinobots have very simple circuitry so they aren't intelligent, but by their strength they become the Autobots that are the most feared by the Decepticons. First only three Dinobots were made, later when those proved succesfull two more were made.

During one of their many attempts to make energon, the Decepticons find a strange object beneath the polar ice. It's a gigantic robot, Starscream remebers him: Skyfire. Skyfire joins the Decepticon ranks, but later when he makes contact with Spike and Sparkplug, he decides to change sides. He becomes very important for the Autobots because in the beginning he is the only one who is able to transport other Autobots by air. The Decepticons discover even more Transformers on Earth. Somewhere deep in the jungle they find a escapepod from their own spaceship that crashlanded milions of years ago. The three Insecticons were on board the pod. These three don't join the Decepticon ranks, they are more of opportunitists and thus only help the Decepticons when it suits themselves.

During one of his adventures with the Autobots, Spike encounters a girl at whom he falls in love; Carly. Carly and Spike even visit Cybertron together, because the Autobots slowly stop funcioning and need new Cybertonium from Cybertron. In the meantime the Constructicons have reached Earth and join Megatron in his quest to destroy the Autobots. Bumblebee and Powerglide make a interesting discovery. Within some sort of energon storm there is a island untouched since the prehistory. It becomes a training ground for the Dinobots. Grimlock gives the island its name; Dinobot Island. Some time after the Constructicons does also Omega Supreme arrive on earth.

The Autobots that hadn't left Cybertron managed to survive all the milions of years that Optimus Prime and his fellows were away. All the girlfriends of the Autobots that had left formed a new group; the Female Autobots. They are still under the leadership of Elita One, who apparently survived the attack on the Autobot base. Megatron gets alerted by Shockwave of the existence of these Female Autobots and he sends a group of Decepticons to capture Elita One.

They succeed in doing so and Megatron orders Optimus Prime to surrender or else he will kill Elita One. Optimus Prime obeys, but in the end he and Elita One manage to escape. Elita One gets seriously injured by using her special skills to save Optimus Prime, so Optimus Prime sets outs to find Alpha Trion. Alpha Trion still remembers the scematics of both Optimus Prime and Elita One and with the use of Optimus Primes powerconverter he manages to repair Elita One.

After yet again a few more defeats, Megatron gets frustrated. He realizes the Autobots are superior on the ground and that he will need some Decepticons that are able to transform into cars if he wants to defeat the Autobots. He then creates five robots that transform into cars and whose outer hull are heavily protected by forcefields. He calls them the Stunticons. The Stunticons are still just machines after their creation and they will have to be taken to Vector Sigma to get their personalities. The Decepticons go to Cybertron over the spacebridge and they beat up Alpha Trion to get his key that leads to Vector Sigma. The Autobots get alerted by the use of the spacebridge and Optimus Prime suspects Megatron sceme. He and some Autobots board Omega Supreme and they head for Cybertron. First they repair the injured Alpha Trion and then they follow the Decepticons.

The Decepticons have already left with the activated Stunticons. To stop the Stunticons, the Autobots make the Aerialbots. Alpha Trion uses his own circuits to activate Vector Sigma without a key. His entire personality is integrated into Vector Sigma. The activated Vector Sigma also gives personalities to the Aerialbots. Not very long after their creation the Aerialbots get trapped in a time trap from Megatron. They arrive just at the start of the war and there they help Orion Pax (see earlier). The Autobots are luckily able to get the Aerialbots back to their own time.

Starscream attempts a new takeover, but once again he fails to get the support of the other Decepticons. Laserbeak dumps Starscream on a tropical island. Starscream finds a lot of old military vehicles from World War II on this island and he gets an idea. He uses the the spacebridge and steals the personality chips of the five renegade Decepticons, those chips were stored there by Megatron. He then returns to Earth and uses the chips and the old vehicles to create his own army; the Combaticons. Starscream finally is able to take command over the Decepticons, but only for a few seconds. The Stunticons appear and their gestalt form (Menasor) is able to defeat Bruticus (the gestalt form of the Combaticons). Megatron accepts Starscream and the Combaticons back into the Decepticon ranks, after some more events.