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I defeated the Pokémon League and went to Route 101 (note that I had the National Pokedex and met Zinnia outside my house at this point) but didn't encounter Prof. Birch. I went to Petalburg and fought Courtney and went back to Route 101. I still couldn't get the Johto starters. Finally I tried after encountering Zinnia at Granite Cave, and still couldn't get them. Why can't I encounter Prof. Birch and get the Johto starters at this point like I should be able to?

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Maybe you should just come back every time you do something in the Delta Episode and see whether that thing you just did was really the event trigger. Bulbapedia once said that my rival appears after I defeat Cynthia, but he didn't, so I tried looking for my rival every time I did something and eventually found out what really made him appear.
I figured it out. It's funny how that seems to happen after I ask the question. Apparently you have to be in your house, then exit and go to Route 101 immediately to grab the starter. It didn't work before because I talked to Zinnia rather than going straight to Route 101.
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I ran into the same issue when I was playing, and I think it has to do with you only receiving the "Help!" message from Professor Birch when leaving your house. Try walking into your house in Littleroot Town, and then walk back out. Professor Birch should yell for help again.

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