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To do scour mission, a suitcase is required. The shop sells it with the limit of one per user.
After buying a suitcase, it is automatically placed in 'key items' tab in your farm. Then, you can access the 'Scour Area' under your inventory. You can then click on 'Send a pokemon on scour mission' button and select a pokemon from your farm. You have to select an area for them to explore. Each pokemon has one like and dislike. You also have to select the time. After sending a pokemon, you will be re-directed to the scour area page and there, you can see whether the pokemon liked or disliked the area you selected for them. A green box or light or a smiley face above the pokemon means they like the area, a red light or box or an angry face means they dislike the area, and nothing means that they are neutral with the area. Note: Despite common belief, a Pokemon's nature / berry preference has no effect on which areas they like and dislike.
You get better items the longer you set the time. Some of the best finds are boxes. You can sometimes find rare items in them. However, you are much more likely to find common items such as evolution or unused items. The higher your scour level is, the higher your chance to get a box. Scour levels are determined by Scour Experience, which can be gained through scouring.
Scouring pokemon can become "tired" if you send them to scour mission continuously. If this happens, you will get a notification on the page where you retrieve them. If you send them out again, they will have an extra bubble over them with a face and they will be less likely to find something. To make this go away, allow your pokemon to rest for a while. As your scouring level grows, the number of pokemon you can send on scour mission increases.
Also, confused pokemon on scour missions eight hours or longer sometimes get "lost"; this means that the scour pokemon will be gone for anywhere from four hours to four days and may come back with something amazing like 10,000 credits, 10 boxes, 20 evolution items, or a new scour area, but may also come back with 0 happiness and nothing. If your pokemon is confused, its name in super mode will be yellow. When they are on a scouring mission they will have a "?" over their head. To confuse your pokemon, view your Party in super mode and use the scroll wheel on your mouse to spin them around very quickly. After spinning they will have yellow sparkles over their head and it will tell you which pokemon are confused. Pokemon will be healed from confusion after they get lost. You can also heal them by using the Yellow Flute or using a Persim or Lum berry, or by trading them to another user.