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Have you tried a Dicelocke? Roll a die when you get onto a new route, and it determines what you do.
Normal first-pokemon-encounter capture happens, plus...
1 - you can also catch the second pokemon you encounter on this route
2 - your new capture goes straight to quarantine
3 - put your highest level pokemon in quarantine
4 - reclaim any pokemon from quarantine
5 - swap one of your pokemon with a quarantined pokemon
6 - roll again - if another 6, all quarantine pokemon are freed
Quarantine is a special box where your pokemon are locked out of the game temporarily. Rolling the die may put pokemon in or out of quarantine, and can really fuck up your plans if your best team member is taken away.
To be fair with this challenge, wait until you have two party members before you start rolling!