This Special Encounter is impossible to get after you restore the city, you must have your seventh badge for this Special Encounter

First make sure you have a Chimecho (you can catch one under the grand stairway in north obsidia) in your party then head over to the Breeding Facility on Azurine Island after you go inside talk to the guy on the left and give him the Chimecho he will then let Chikorita open, go to the back and Chikorita will be in the cage to the left just interect with the bars and they will open.

Alternative Way Edit

Another way is to donate enough fund to get the Azurine Nature Center then fly to it and go to the balcony on the top floor, there should be a scientist to the right speak to him and he'll tell you about how he found a chikorita locked in the basement.

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