They kidnapped the Parrots from Parrot Castle under the orders of their leader, the Commander of Darkness. According to Parrot King, the Soldiers of Darkness leave skull marks wherever they go. Jumpy Ghostface and Parrot King accidentally discover their underground base where they are captured and brought to the Commander. They try to reason with the Commander but he does not care if they have reformed.
During this encounter, Jumpy Ghostface blows out the candle the Commander of Darkness wears on his hat, revealing the Commander has nyctophobia (a fear of the dark which Jumpy & Parrot King find funny). The Commander imprisons Jumpy and Parrot King, but they and the other Parrots are freed by the Zebra Brother's and their Zebra Clone Army (Jumpy & Parrot King however are captured by the Zebra Clones).
The Zebra Clones knock over the Commander's candles, causing him to order a retreat. While they are fleeing it is revealed that there are only 6 Soldiers of Darkness (including the Commander).
After being defeated and losing their Zebra Clone Army to the Butterflies, the Zebra Brothers run into the Commander and Soldiers of Darkness, who take out their anger on the pair.