Disclaimer: I do not own Detective Conan nor the concept of Hanahaki disease.
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The moment he started coughing up flowers was the moment he knew there was no way he had a chance of returning to his old life.
There was no way he would live long enough to tell her of his secrets for she had finally moved on.
He would never know if she would have given him forgiveness or condemnation for those very same secrets.
He knows he could always just have surgery to have the flowers removed but he doesn't ever want to lose these longheld feelings for her even though it only causes him pain now.
The flowers may be a sign of his unrequited love but it is also a sign of his love for her.