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'Say Farewell' is the command given when the leader wants the target Pokemon to leave the team forever. Pokemon that are given this command will disappear from the team forever, unlike 'Stand By' which only commands the target Pokemon to stay in its Friend Area. Legendary Pokemon that is commanded 'Farewell' can be fought and recruited again. 

Methods

There is only 1 method for giving this command. However, there is a second way for Pokemon that are just recruited. 

Method 1

Works for all Pokemon except the starter and the partner.

In the example, I used a snorunt as the target Pokemon and Latias as the team leader.

1. Go to the friend area where the target Pokemon rests.
Farewell 1







2. Face the target and press A or B. A menu should appear. Select 'Say Farewell'.
Farewell 2







3. A question will be asked. If you want the target to leave, select 'Yes'. If not, select 'No'.
Farewell 3and4







5. If yes is selected, a text box should appear:
Farewell 5







6. After that, the screen is refreshed. The leader reappears at the entrance of the friend area and will no longer find the target Pokemon at the spot where it once rested.
Farewell 6