Shadow Pokemon is a pokemon who is capable of entering shadow mode. Currently the only place where these pokemon can be found are Decolore Islands.
For years team Rocket is controlling Decolore Islands, and they are investing huge amounts of money in Shadow Pokemon project. With HQ in Grand Spectrala Island, they hold a huge dark gem that works only on this islands area. They've been working on many pokemon to test their project, and they found out when pokemon is in great rage and hates almost everything, with the power of Dark gem it enteres
Shadow stage. What it does it raises all its stats by 40% almost. And when they succeeded, they started working on their main objective- legendary pokemon Lugia. At first Lugia managed to resist, but nothing lasts for ever and it got turned in to
Shadow Lugia.
Shadow Lugia still swims within deep ocean in Decolore Islands causing havoc, waiting for someone to save it.
Today many trainers come on these islands to make their pokemon enter shadow stage. By now if pokemon is really bonded with its trainer, their shadow stage can't change their heart and personality. And if they got lucky to stop team Rocket and rescue Shadow Lugia.