Lines 25-28 Summary

Get out the microscope, because we’re going through this poem line-by-line.

The Bat that flits at close of Eve
Has left the Brain that won't believe.

Now, we're still dealing with an animal—just not one that's being abused or tortured. Maybe this comes as a relief?
The bat is still "a world in a grain of sand," though—it's more than what it first appears to be. Particularly, it symbolizes a thought (or something) emerging from the mind of an unbeliever.
Blake was a Christian—though a very unorthodox one—and didn't take too kindly to atheism, as this couplet makes clear.
Maybe Blake chose bats because they're usually considered spooky or because they're said to be blind (even though no bats really are totally blind; but the idea makes sense, since being an unbeliever, in Blake's view, would make you blind to spiritual realities). Whatever the reason, we're supposed to imagine this bat flying out of an atheist's mind—which you might picture as some sort of attic or crumbling tower that only has old junk and bats in it. Could it be that the bat symbolizes a doubt flying out from this skeptical mind?
Also, is there any greater symbolism to the fact that the bat is flitting around at "close of Eve"? It's a classically eerie time of day, but Blake could also be suggesting that the bat's unbelieving attitude is something that leads toward a deeper darkness or a state of mental decline.

The Owl that calls upon the Night
Speaks the Unbeliever's fright.

Even though scholars say that these couplets were (more or less) randomly gathered together by Blake from his notebooks, you can still see how there's a kind of order. Like, right here—he's talking about an owl and atheism, right after talking about a bat and atheism. He's not done riffing on flying, nocturnal animals that symbolize not believing in God.
How does the owl sound like it's speaking "the Unbeliever's fright"? It seems like this "fright" is a kind of cosmic, existential despair. You're worried that there's no higher purpose, nothing out there in the dark. Maybe Blake's thinking that the owl's cry of "Hoo!" sounds like a question, "Who?" The owl might be wondering who, in the night, is responsible for creating the world. (Of course, "the Unbeliever's fright" can also be expressed through undeniably catchy pop rock.)