The Autobots go on alert as the Decepticons return to Earth in the series opener, Meanwhile a group of humans find themselves with new caretakers after stumbling into the middle of the Autobot conflict with the Decepticons.
The Autobots go in search of Cliffjumper, whose life signal is weak and find Megatron wielding the dangerous Dark Energon.
The Decepticons, in order to find the Autobot base, capture and torture Secret Agent Fowler, and it's up to Bulkhead and the three human kids to track him down. Meanwhile, Megatron raises an army of undead Transformers.
The kids, along with Bulkhead, Arcee and Bumblebee storm the Decepticon ship to rescue Agent Fowler, and come across the blueprints for a secret plan. During this, Optimus Prime and Ratchet fight against Megatron's army of undead Transformers.
Through his Space Bridge, Megatron raises the dead Transformers of Cybertron, and summons them to Earth. The Autobots have to find a way to sabotage the Bridge, or else their new home will be destroyed by the legion of undead Decepticons.
Starscream has interests in being Decepticon commander, after the previous death of Megatron. He awakens Skyquake, a Decepticon who's leader is truely Megatron. While Optimus and Bumblebee have a battle with Skyquake the other Autobots help the humans with their science projects, for their science fair.
When Bumblebee and Bulkhead go to the Arctic they find a Cybertronian Pod. They bring the pod back to base. Optimus and Arcee later go on patrol back in the Arctic. When the humans come over to Autobot HQ Raf finds a tiny metal robot. He shows Bumblebee, Bulkhead, and Ratchet the robot. The Autobots jump in fear as they see the robot. They explain that the tiny being is a Scraplet, a small metal eating robot. The Scraplet attacks the Autobots but is defeated. Ratchet finds out the pod that Bulkhead and Bumblebee had found was a Scraplet trap which had been sent into space many eons ago and landed in the Arctic. While Optimus and Arcee contact HQ to return back there is no answer and the two Autobots are stuck in the Arctic. If Ratchet does not open the Ground Bridge Optimus and Arcee will die. The Ground Bridge isn't working because the Scraplets had chewed a big whole in it. Raf, Miko and Jack fix the Ground Bridge successfully and Ratchet is able to open the Ground Bridge. But the Scraplets attack and Bulkhead makes a distraction leading the Scraplets into the Ground Bridge. When the Scraplets enter the Arctic they freeze to death and Optimus and Arcee return back to HQ. As Ratchet and Optimus talk as how strong the humans had been Miko screams in fear. The final scene shows that there is a spider and Miko is scared.
When the Autobots recieve a signal from a starship which has entered the Earth's Solar System the owner of the starship is intentified as Wheeljack. Wheeljack is Bulkhead's best friend back on Cybertron. Bulkhead and Wheeljack went on many adventures together and were part of the Autobot warrior fighting group The Wreckers. Meanwhile, Starscream sends a Decepticon named Makeshift on a mission, to pretend he is Wheeljack in order to locate the Autobot Base. When Wheeljack arrives somewhere on Earth he is attacked by Vehicons. The Autobots pick up his signal, once again and Arcee, Bumblebee and Bulkhead Groundbridge to where Wheeljack is to save him. But, Wheeljack defeated all the Vehicons before the other Autobots could help him. Then, it is shown that the real Wheeljack has been captured by Starscream and is held personer. Later, Bulkhead and Wheeljack (who is Makeshift) party. When Bulkhead and Wheeljack play a game of ball they acciently destroy the Groundbridge. Wheeljack asks Ratchet how long it would take for the Groundbridge to be repaired. After, Bulkhead tells stories about his adventures with Wheeljack. To Bulkhead for some reason Wheeljack doesn't seem like himself. Miko takes Wheeljack on a tour of the base. He asks Miko where is the Autobot Base is located. She tells him the correct answer, outside Jasper, Nevada. Bulkhead thinks something's wrong with Wheeljack so he tells him to tell the story about Darkmount Pass. Wheeljacks tells the story correctly, except for one thing he said Bulkhead was there and Bulkhead wasn't. Makeshift's cover is blown and he threatens if the Autobots do anything he'll kill Miko. The real Wheeljack escapes and he defeats some of Starscream's army that he has prepaired on Groundbridge to the Autobot Base. He Groundbridges to the Autobot Base and has a fight with Makeshift. Makeshift loses and is sent back to the Nemisis. Just before he tells where the Autobot Base is he realizes there is a bomb on him and he blows up. The next day, Wheeljack leaves, but asks Bulkhead if he wants to come with him. Bulkhead says no and the last scene shows Miko taking a picture of Wheeljack and Bulkhead.
The Autobots assist Agent Fowler in transporting an implosion device. But when a group of vehicles attacks them they are identified to be Humans and not Decepticons. The assailants are identified as M.E.C.H. led by Silas.
The Autobots pick up Energon signals in Greece. Miko and Bulkhead go and investigate. There are massive Energon readings. But, Bulkhead sees a picture of Greek Gods...but Bulkhead sees something...Cybertronian, a Energon Harvester. Then, Breakdown (who has a history with Bulkhead) attacks them. Breakdown returns back to Decepticon Base. Meanwhile, Starscream has a meeting with Knock Out and gets him and Breakdown to help him find the Energon Harvester. Bulkhead and Miko report back to Base about the Energon Harvester, and Optimus explains that the Energon Harvester can easily harvest Energon, from anything. Raf finds the Energon Harvester and it's location is in a museum. Miko, Jack and Raf Groundbridge to the museum and try to get the Energon Harvester. The Autobots wait outside the museum and Breakdown and Knock Out distract them by having a battle with them. Soundwave steals the Energon Harvester and Miko is caught by a Security Guard. The Autobots, with Raf and Jack return back to base. Optimus gives Bulkhead orders of staying at base and not doing anything. Bulkhead denies Optimus and Ratchet builds a replica of the Energon Harvester. Bulkhead remembers about massive Energon readings in Greece and Groundbridges there. He finds Starscream, Knock Out and Breakdown. Starscream tries to harvest Bulkhead's Energon, but Bulkhead destroys the Energon Harvester. Starscream retreats and Bulkhead is found by the rest of the Autobots. Miko lies to the Security Guard and Agent Fowler arrives and gets Miko out. Suddenly, the Energon Harvester has returned and the Security Guard is confused. The Energon Harvester is actually the one Ratchet made.
Knock Out starts to develop interest in Human illegal car racing. One day, Sierra asks Jack for that ride on his motorcycle, as Jack promised. Although, Jack tells Sierra not this time and Vince (sometimes refered to as the bully) tries to show off and give Sierra a ride. Vince asks Jack to go racing. Arcee doesn't want to do it and Jack doesn't take the offer. Until, Vince talks about how "ugly" Arcee is. Arcee gets angry, and tells Jack to tell Vince it's on. Later that day, Vince and Jack go racing. Jack ultimately beats Vince. When, Arcee and Jack return to Autobot Base, Raf and Miko tell Jack that everybody at their school knows about Jack and Vince's race. The next day, Vince asks Jack to go racing again, Jack doesn't want to, but he eventually takes Vince's offer. Arcee disagrees with Jack, and doesn't go. So, Jack asks Raf if he came borrow Bumblebee. That night, Jack and Vince enter a illegal car race. But, Knock Out enters too and he tries to terminate Bumblebee. Bumblebee does some crazy things and Vince is amazed. After losing Knock Out, Vince goes up to Jack and asked him what just happened. Until, Knock Out anciently thinks Vince is Bumblebee's Human friend, so he kidnaps Vince, right in front of Jack and Bumblebee. Bumblebee calls for backup, and Arcee, and Bulkhead come to help. As, the Autobots track down Knock Out, and battle him. Knock Out escapes. Meanwhile, Optimus wonders where the others have gone, and asks Miko, and Raf. They act like they don't know anything, but Optimus finds out. So, Optimus makes an appearance to stop Knock Out, succeeds. Later, Knock Out returns to the Nemesis, and Starscream gives him a punishment, after not obeying his orders. Jack and Bumblebee drop Vince off at his car. The next day, Sierra asks for that ride again, and Jacks says no. But, Arcee feels bad and lets Jack let Sierra have a ride.
Arcee takes Jack along on a seemingly routine mission but when her nemesis Airachnid turns up, Jack becomes a liability she needs to protect.
Optimus Prime becomes infected with a Decepticon plague and Arcee and Bumblebee must sneak aboard the Nemesis to find the formula for the cure.
In the continuing story from “Sick Mind”, Megatron has escaped his damaged body in the mind of Bumblebee.
Kids are trapped in an alternate dimension with a reanimated Skyquake in the middle of a GroundBridge failure.
When Breakdown is captured by M.E.C.H. (to see what makes the Cybertronians tick) it's up to the Autobots to save him.
Airachnid plots her revenge against Arcee and Jack by negotiating with Silas and M.E.C.H.
The Autobots try to claim a magnetic weapon before the Decepticons get to it.
The Autobots, with Jack and Miko, fall victim to an Energon mine cave-in and find themselves trapped with Starscream and Megatron.
The team is surprised to learn that Starscream wants to become an Autobot.
The Decepticons hunt Bulkhead down when he gains possession of the secret formula for synthetic Energon. Unfortunately, the data inside his head is slowly erasing portions of his brain. Unless the Autobots can come up with a solution, Bulkhead will never be the same.
Ratchet's devotion to the Autobots is tested when he believes that he has perfected the formula for synthetic Energon. But when Ratchet uses himself as the test subject, the synthetic Energon begins to alter his personality.
When the Autobots learn of the Decepticons' plans to build a Space Bridge, Optimus decides to face Megatron once and for all.
The Autobots discover that Dark Energon is responsible for Earth's recent natural disasters.
The Autobots team up with a surprising ally to save Earth.