Professor Willow and the team leaders have been hard at work observing and researching these happenings with Team GO Rocket, and they’ve come up with a plan to restore the PokéStops and rescue the Shadow Pokémon!
2. Battle Team GO Rocket — Once you begin the encounter with a Team GO Rocket Grunt, they’ll challenge you to a battle. We’re counting on you to accept their challenge and defeat them!
3. Catch the Shadow Pokémon — After a successful battle, you’ll have an opportunity to catch a Shadow Pokémon that Team GO Rocket carelessly abandoned. Candela and Professor Willow discovered that these Pokémon look unusual and behave strangely because Team GO Rocket tried to make them stronger through unnatural means. After additional research, Professor Willow has also found that Shadow Pokémon can’t be traded away by the Trainer who rescued them unless they’re Purified first!
4. Purify the Shadow Pokémon — Thanks to all your research, Blanche and Professor Willow have discovered a process called Purification. Not only does Purification help Shadow Pokémon return to a more normal state, but Purified Pokémon can also become stronger than their normal counterparts due to the gratitude they feel toward the Trainer who saved them!
Source: Official Pokémon GO blog