Ninja does not need to be bullied! This drains her confidence and can start severe behavior issues. She was there first .. this new little girl is infringing on her territory and she doesn't like it. Your first mistake was thinking your Ninja needed some company. Many cats prefer solitude and quiet and they don't need a playmate. Now this playmate is aggressive and dominating and making Ninja's life miserable. I feel so sorry for her.
The introduction process did not go well. You can try to start over, but it's probably not going to go much better. There are some things that might help. Make sure each cat has their own territory. Make sure there are no dead ends so that Ninja is cornered. Make sure you have at least two litter boxes, preferably three so they do not have to share. You obviously have cat tree. I have one cat and he has three of them! So you may need another one.
Do you play with each of them together? Are you wearing out your bengal's energy? Do you divert it away from Ninja? It's fairly common that a bengal will dominate -- and your bengal is still very young and will grow. You're going to have to step in and make some changes so that each of your kitties is happy.
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I know Jackson Galaxy has dealt with this on many of his My Cat From Hell shows and I believe you can view some of then online. You may get some ideas. I hope you're able to solve this problem before Ninja just gives up hope. I always feel bad for a cat who is being terrorized by another cat. I wish you luck!