Your photo is too close, so it makes it difficult to see. To be honest, the total and uniform browning looks like fireblight, but it's hard to say for sure. Honeycrisp is somewhat susceptible to fireblight, but I think this usually manifests itself before now in Z6, but again...I say usually.
This issue doesn't appear to be a recent development, as it seems that fungal spores are now evident on the dieing/dead branch tissue.
Does the end of the vertical exhibit the tell-tale shepherds hook? If it does, it's most likely fireblight.
At any rate, diagnosis be damned, cut back well below all damaged tissue and completely discard the material. Get it out of your orchard, burn it or bag it for the trash.
It also could be just a neglected case of mildew of which our Z6 climate has been much more predisposed to as of late.

Here is another photo hopes this helps.

Here is another photo.

It appears to be Fireblight in my opinion so I would cut off that section and several inches below ASAP and destroy what you cut off by burning it. I'm not aware of anything else that looks like that.

Well, I hate to contradict Clark, but it doesn't look like any fireblight I've experienced.

I've never seen fireblight affect only leaves in the middle of the shoot, like your photos seem to indicate.

My guess is you have the later effects of Honeycrisp yellows, a unique disorder which affects Honeycrisp.

It could be hopper burn, but probably Honeycrisp yellows.

The tree looks like it is in somewhat poor health. I'd probably recommend a mild fertilizer, as well as making sure the young tree isn't forced to compete with grass/weeds around the base of the tree.

If it's especially dry during the summer, it might be a good idea to give the young tree a drink every once in a while.

Is that fungus on the trunk? The picture is a little blurry. Is there any sign of physical damage on the trunk?

I've heard of trees getting infected with fungus as result of drought stress, but the other leaves don't seem to indicate drought issues. Leaves usually turn color and fall off.

That's not Honeycrisp yellows or any associated effects. The leaves don't even show the normal yellows like mine have this time of yr.

Not sure what is going on but would like to know what's on the bark. It's closer to fire blight than the yellows.

Is the bark healthy under the area where those whitish pustuales are located? Any evidence of insect feeding on the blacked leaves? Sorta looks like an area affected by webworms.

This post was edited by fruitnut on Wed, Oct 1, 14 at 11:36

Seeing the additional photos I agree with olpea in that it's not fireblight.
I also agree with fruitnut in that it's definitely not a Honeycrisp disorder (HC yellows).
I think it was a case of mildew left untreated. It appears from the photo that the tree is in a lot of shade at the time of the photo and as olpea mentioned it looks as though there may be a lot of competition from other plants.
To my original suggestion, no matter what it is or isn't I'd cut back well below the damaged tissue and discard. I'd also look to move it to a better location if possible.

"That's not Honeycrisp yellows or any associated effects. The leaves don't even show the normal yellows like mine have this time of yr."

Fruitnut,

Just to clarify, I mentioned the later effects of Honeycrips yellows. I've never seen leaves turn brown before first turning yellow. These leaves were yellow earlier in the season.

I think the poster potentially missed the earlier problems with this foliage (i.e. yellow leaves) which eventually desiccated and turned brown.

This post was edited by olpea on Wed, Oct 1, 14 at 14:19

olpea:

They really aren't yellow, rather moddled. It looks like a virus infection. And some leaves above and/or below would likely have the moddled pattern.

This is Honeycrisp yellows. I don't expect these leaves to brown or fall off early.

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Another pic of yellows.

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This is another variety on same tree not yellows. These leaves are falling off from the middle of a shoot. I don't know what issue is involved.

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I think fire blighted leaves can turn brown without yellowing first. But not likely in the middle of a shoot. Orchardman's problem probably isn't fire blight or HC yellows.

This post was edited by fruitnut on Wed, Oct 1, 14 at 14:46

Here is a pic of one of my Bartletts w/ some significant fireblight this season. I left the fruit on the blighted shoots because I figured it wasn't worth picking. Notice whole shoots are blighted.

Fruitnut,

Here is another pic of another Bartlett, w/ much lighter fireblight strikes. Again whole shoots are blighted.

Yes and those brown leaves that are stuck on the tree didn't turn yellow before turning brown.

Beyond the fact that the whole shoot died, what's your point?

All I questioned about your initial comments was about HC yellows being the cause.

Leaves that turn yellow before turning brown fall off. If they go green to brown like your blighted shoots or Orchardman's leaves, they stay attached because the absicission layer never had a chance to form.

This post was edited by fruitnut on Wed, Oct 1, 14 at 15:33

"Beyond the fact that the whole shoot died, what's your point?"

My point is that the symptoms based on the pics of the OP do not suggest fireblight to me.

I respectfully disagree with your comment, " It's closer to fire blight than the yellows."

Perhaps it's not the yellows, but just because you haven't experienced browning of yellowed Honeycrisp leaves which cling doesn't necessarily indicate others (in other areas) have not. I've seen Honeycrisp photos of much more severely yellowed leaves than your own pictured (in other words a more severe case of Honeycrisp yellows).

This post was edited by olpea on Wed, Oct 1, 14 at 16:13

Oplea:

"I've never seen leaves turn brown before first turning yellow."

Next year keep a better eye on your blighted shoots. You'll see something new.

Fruitnut,

It appears our posts/edits were overlapping earlier, which makes it a bit confusing to follow.

One thing we can agree on is that it's probably not fireblight.

And yes, fireblight can affect shoots so rapidly to turn them from pretty much a wilted green to brown.

Olpea I'm glad you did say that because it seemed strange to me that tip wasn't dead yet as well. The white dots suggest fungus. I can't see very well by the photo but what I thought was happening was Fireblight in the wood (eg. Small lesion from the year before growth) or spread by bug , deer, bird etc. In this link is an example picture which is one of the reasons I did not rule it out as fire blight. As Appleseed70 mentioned regardless cut it back and get rid of the problem. Fungal instead of bacterial is possible but I've never seen any fungus like that. On a side note my cherries all had dead tips and so I went to look what the problem was and grasshoppers girdled the tips. Not at all what the problem looked like from 7 - 10 feet away.

Here is a link that might be useful: fireblight

This post was edited by ClarkinKS on Wed, Oct 1, 14 at 20:30

Thanks for the help gentlemen. The damage seemed to happen almost overnight. I cut off the damaged portion and disposed of it.