Shadows of Fear: Return of Cipher is the sequel to Morpher01's first fanfiction, Shadows of Fear. It continues the adventures of Skull the Shadow Marowak as he protects not only himself and other Pokémon, but his five-year-old son, Cubon.
The sequel takes place five years after the original, therefore five years after Pokemon XD: Gale of Darkness. As such, canon elements are still somewhat common, though non-canon things are still seen.
Better than before
Since Morpher's writing has vastly improved since his first attempt, the fiction became more of a hit than its prequel, with better pacing and action. The lighter side of Skull's personality shows, as he is revealed to have a wise-cracking side.
New and improved Shadow Pokemon
As proven from the first battle within the fiction, Cipher has improved their Shadow Pokémon with the usage of a device created by the Admin named Ein. In addition to removing and replacing memories, the device also gives Shadow Pokémon eyes that blaze with dark energies. It is unknown whether a human without any special ability can see the new additions to a Shadow Pokémon, but the ruthlessness and lack of mercy are entirely clear to all.
First multi-fic crossover
Somewhat late in Return of Cipher, Morpher and fellow Serebiiforums user Gazmof agree on a crossover with their two fanfictions: Morpher's Shadows of Fear: Return of Cipher, and Gazmof's Watchers of Raikou. Ultimately, it was a success, and both users enjoyed it quite a bit.
Cipher's last hurrah
As the fiction begins to draw to a close, Skull tricks a Slaking belonging to one of Cipher's leaders—namely Evice—into using Earthquake one too many times, causing all of Citadark Isle to shatter into many pieces. Skull escapes easily, though his son is not quite as lucky. Cubon is alive, though suffers an experience somewhat close to death, having floated all the way from Citadark Isle to Gateon Port, unconscious throughout the entire journey. To his father's relief, Cubon is revived merely by several pounds on the chest.
As Skull rests, he is unwittingly captured by Michael, the protagonist of Pokemon XD: Gale of Darkness, whom Skull believed to be dead. Later, in a fit of rage, Skull's Reverse Mode activates and he brutally kills not only Michael, but his sister Jovi, whom Michael had given Cubon too. Skull then takes Cubon and moves to Hoenn, seeking to avoid humankind for good.
Third time around
According to the Fanfiction Commercials Thread on the Serebiiforums, there will be a third installment to the series. It will be titled Shadows of Fear: Journey with a Brain, and will further chronicle Skull's adventures.