Learn Turkish: Bebek şimdi ağlıyor. - The baby is crying now.

This happens because of a rule called vowel narrowing. When a verb root ends in a wide vowel like a or e, and you add the -yor ending, that final vowel narrows down. The a turns into an ı, so ağla- becomes ağlıyor.

Where is the personal suffix for "he/she/it" on ağlıyor?

There isn't one! In Turkish, the third-person singular (he, she, or it) doesn't use a personal suffix. Just having the present continuous suffix -ıyor on the root is enough to mean "is crying".

Why is the word şimdi (now) in the middle of the sentence?

In Turkish, the verb usually goes at the very end of the sentence. Time words like şimdi often come right after the subject (bebek) or at the beginning of the sentence. Both Bebek şimdi ağlıyor and Şimdi bebek ağlıyor are perfectly natural.

Why isn't there a word for "the" before bebek?

Turkish doesn't have a definite article like "the". When a noun like bebek is the subject of the sentence, it is usually understood as specific ("the baby"). If we wanted to say "a baby is crying," we would add the word for one: Bir bebek şimdi ağlıyor.