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You send it to iBooks by opening it in the app.
Example:
If the file is opened in Safari, you'll get "Open in iBooks" at the top right. If you don't see it there, tap once to make it appear.
View attachment 60973
When you tap this, iBooks will open, and the file will be saved to the app.
The file should open iBooks. If everything works right, Safari will close, and iBooks will open, all by itself.
See if force closing the app will help:
Double tap the Home button to reveal the multitask bar, then slide the iBooks app towards the top of the screen.