Episode 2 of Transformers Prime, Darkness Rising part 2, begins with a summary of the first episode before jumping back to the Decepticon ship which is hovering over a mountain on Earth.  Starscream has found an large Energon deposit and is stockpiling the Energon.  Megatron isn't interested and announces to his fellow Decepticon that he has found "the blood of Unicron" AKA Dark Energon.  Starscre­am lets the watchers know that, if legend is true, Dark Energon can raise the dead and presents the body of CliffJumper to the Decepticon leader to test whether this claim is true.

Meawhile back on Earth Optimus Prime finishes telling the Humans that the Decepticon's could be after them and so, for now, the Autobot's will protect them.  At this point the alarm rings in the base warning them that Special Agent Fowler has decided to give the Autobot's a visit.  Agent Fowler is Earth's liaison office to the Autobot's.  Prime tells the kids to hide whilst the Agent arrives to remind the Autobot's that they are suppose to be in hiding and to confirm that the Decepticon's are back.  The Agent tells the Autobots to "handle this" or he will.

The scene changes once more as Megatron revives Cliffjumpers fallen body as a Dark Energon infused zombie.  As zombie-jumper destroys some Eradicons Starscream begins to cower as Megatron slices Cliffjumper in two.  The test proved successful and, if he can learn how to control it, Megatron realises that he has an ultimate weapon.  What Megatron doesn't realise is that by bringing Cliffjumper back online, the Autobots pick up on his signature and so with hope that their comrade made yet still be functional Optimus Prime, Arcee, Bulkhead and Bumblebee head off through the land-bridge to the source of the signal.

Ratchet is less optimistic and feels that it is just a bug with the human technology they are using within the Autobot base.  The humans remain behind with Ratchet and when the Autobot runs into more bugs with the computers Raf, the youngest child, uses his laptop to fix the computers.  The computers are described as ex-military, and yet they seem to have no security.  Ratchet offers to ground-bridge the Humans to Japan to meet Miko's parents, and get them out from under his feet, but they decline.

Meanwhile the other Autobots are on the trail of Cliffjumper's signal and soon run into the Eradicons and a full scale battle commences. Realising that his nemesis has arrived, Megatron orders the Decepticons retreat so that he may concentrate on finding a way to control the Dark Energon.  He orders Starscream to blow-up the Energon mines hoping that it will destroy the Autobots as well.  As Starscream looks to carry out his leaders wishes, Arcee spots the body of the fallen Cliffjumper on a platform inside the base but soon realises that this is not the Autobot she new but something else.  As the remains of zombie Cliffjumper falls on top of the Energon crystals Starscream detonates a bomb blowing up the mountain but not before the Autobot's can use the ground-bridge to escape back to the base.  Within Autobot base Arcee explains what she saw but starts to feel faint.  It's at this point that the Humans realise that there is more to the Autobot's than normal robots.  Ratchet takes a sample of Dark Energon from Arcee who has some on her from when she found Cliffjumper.  Jackson interrupts things pointing out that his parents will notice that he is not back yet and Prime orders the Autobots to take each of the Humans home but to stay with them and guard them.  Bumblee goes with Raf, Bulkhead with the excited Miko and Arcee with Jackson (after Ratchet says he's too busy).

The scene shifts once more to Jackson's house where he and Arcee start to argue about each other problems before Jack's mother turns up.  Jack says he's 16 and bought the motorbike 2nd hand and that it needs repairs.

Morning dawns and Arcee revs her engine to wake up Jack saying that they have to head back to the Autobot base.

The scene shifts once again back to the Decepticon ship where, believing he has destroyed the Autobot's, Starscream brags to Megatron however the Decepticon Leader points out that they have thought that they have destroyed Optimus before.  Megatron decides to test the Dark Energon upon himself, much to Starscreams panic but before we can see the results, there is yet another shift this time Ratchet's lab within the Autobot HQ where he is running tests on the substance he pulled from Arcee (he does not realise that it it Dark Energon).  Some falls loose landing on a piece of equipment in his lab which then turns to life in the form of a small insect like creature similar to Scalpel from Transformers Revenge of the Fallen.  The credits then roll.

All in all this is a good continuation of the Darkness Rising story and progresses both the relationship between the Autobot's and the Human's as well as the plans of Megatron.  Once again Bulkhead has little screen time, but Ratchet grumpy character gets the chance to be highlighted.  For the Autobot's, Arcee continues to be the main character along with Jack Darby and its confirmed for anyone that may have doubted it, that Cliffjumpers appearance was purely as a cameo so fans of his will have to wait until the IDW prequel comic series to see action from him.