"The soil is wet" is the problem. Little 'bonsai' junipers from big stores (Wal-Mart, etc.) which I'll assume for this posting is where you got your tree, are 99% planted in gunk - peaty potting soil (if that) that holds water all the time instead of letting it run right through - which it should - and so your roots have probably rotted away. Junipers need a lot of the soil to dry out between waterings - they're not African violets - and having taken it indoors (out of good air circulation, full sun, etc.) and kept it 'wet' was asking for trouble. Plus if it had/has a layer of pebbles glued on top that should have been pried off the day it came home to allow you to judge dryness, and not grow mold underneath. Plus you apparently know it needs to be outdoors, but that alone (with conditions otherwise ideal) wouldn't have killed it, but the water and lack of full sun and 'air' plus indoor dryness did. Unless it still feels soft and flexible (which I doubt), I suggest you just chalk it up to learning and bad luck, and when you settle in your new place, get another one, but whatever kind you get, do some reading first, as they all have different needs. See if you can find a local club to join - the best and fastest way to learn. Oh - I should also say that rather than peat/potting soil a 40/60 mix of coarse loam from a garden centre and small size gravel for aquariums would be better, allowing water to run thru - and don't let the pot sit in the drain water. I think it's probably too late for your tree to bother with repotting, etc. now, but keep it in mind for future. Sorry!

Usually when a Juniper starts looking like it is in trouble it is too late. Lucy is most likely correct, this tree is Kaput.

I know how you feel losing a special tree and you would do anything to save it. My 80 year old horticulturist friend has a 2 acre farm devoted to maples mainly. It floods during heavy rain and when the weather is dry the water-table is just a mere 10". So root rot is common and he gets moody the whole day when he loses one tree out the the hundreds he has.
I told him it is possible to save some of these dying trees if you take action fast enough. So I had many encounters with fighting root rot cases. I fancy your chances of saving this Juniper rate about 10%. Anyway according to Lucy and Vance, your tree is kaput and I fully agree.
However this is what you can do to pull through with that slim 10%. You may speed up the death knoll for the tree, anyway if it is not gone now, it will be soon.
The important thing is to inspect the roots themselves. Most likely the fibrous roots are all kaput. But look at the larger roots, if they still show green then your 10 % is still there. Also observe the root crown; if it shows any sign of rot then the 10% is gone even if it has green tap or branch roots. If you can see a good crown and green larger roots, then remove all soil completely by water pressure. Prune the roots generously making sure you do not leave any rot tissue on them. Even a speck of this rot tissue will start spreading and kill your tree as its resistance to disease has been compromised.
Then give the roots 3 rinsing of any commercial fungicide and allow them to dry in low humidity area for half a day. Then you pot it using a highly porous sterile medium. For me I find the best is perlite as you want the water content to be the lowest possible. You must ensure that the medium never dries out.
My experience has indicated that even with all these stringent measures, you should be happy to get 20% to survive. I sometime wonder if it is not better to go out and buy a replacement tree. It is difficult if you have become attached to your tree.
Be positive sunshine and I wish you luck.

Oh, Sunshine
I forgot to mention to you to chop off as much foliage as you can afford to reduce the water demand. Keep sufficient small branches to maintain the plant's form as Juniper seldom rebud below their growing points. With maples I lope off all and retain about a foot of the bottom trunk. Now this gives me an opportunity to adopt the 'Chop trunk technique'. Wonderful!!

No don't chop the foliage... all that does is stress the tree by telling it to grow new branches and needles, and you really don't want to do that right now. Water demand is not a problem with junipers anyhow, and if it was overwatered to begin with, it needs to use up whatever it has, not hang on to it.

Lucy,
An interesting point though controversial.
When root rot sets in, the plant is dying from lack of water because osmosis is absent in the roots. Therefore you need to conserve the little reserve of water in the above ground plant tissues. IF the foliage is there then photosynthesis automatically commences and makes its water demands. Removing photosynthesis or in this case of Juniper reducing the rate of photosynthesis helps to conserve the water and the plant then can direct it to root growth, as all living tissues is made up of 75% water. With plants in the ground the lower trunk invariably holds enough food reserves to devote to growth to satisfy the plant's needs. Plants knows how to prioritize its needs and here human hands can help to accentuate its area of needs.
I have to admit the above statement is based on logic and not on research I have conducted. Thus it is open to errors. Perhaps I may have the inclination to conduct experiments to test out my theory.

Jam, water uptake is driven by the transpiration-cohesion-tension mechanism. Essentially, as water is lost through the leaves, it "pulls" water through the veins, through the stems, the trunks, the roots, and then from the soil. Roots rot because of being too wet, too long. Thus, by reducing water demand (through cutting off foliage), the roots stay wetter, longer. This is generally not good.

That is also why Walter Pall argues that newly collected raw stock (i.e. yamadori) should not be planted in massive grow boxes. Rather, they should be planted in grow boxes which accomodate the existing rootball with little excess soil. The plant has reduced water demands, meaning that any excess soil will simply hold excess water, which can lead to root rot.

-Audric

then check out this link from University of Illinois from Chicago:

Transport in Plants.

Check out the diagram under the section "Transport of Xylem Sap," called "Transpiration-Cohesion-Tension: A Mechanism to Pull Xylem Sap up the Plant."

(This is what we covered in our last bio lecture!)

-Audric

Audric,
Your lecture 10 is most interesting. I did biology in college such a long long time ago, that the details covered in lecture 10, makes our lesson fell like scratching the surface on water transportation in plants.
In the case of sunshine's Juniper, you mustn't forget that the root rot has destroyed all the root hairs; no root hairs no mycorrhizae and no surface area for absorption. Thus if you allow photosynthesis then transpiration in stomata would deplete whatever water reserves that exist in the plant cells. The result is you only get water loss but no water intake for replacement. Thus the plant will die.
The method I proposed is to reduce water loss through the stomata, conserve the water reserves in the Juniper cells and use it to grow hair roots. If hair roots appear I may have saved the day, as osmotic pressure suffices to supply water to a height of at least 5 feet. That's the reason why I advise lopping off the maple trunk and keep no more than 2 feet of trunk. The question still remains as to whether the tree still possess enough reserves to sprout new foliage to continue building up its food replacement. That is why we must attack the root problem before they destroy the root hairs completely. Even then we must decrease the leaf foliage in direct proportion to the root hairs lost, as reduced surface absorption area means a reduced osmosis volume no matter how great your transpiration-cohension-tension might be.
Thus my method offers the best chance to save the Juniper, I would think so.

Jamkh - Possibly you don't realize (it took me a while!) that this subject along with trying to tropicalize maples, and a whole lot of other scientific issues have long been studied by many, many horticultural people and bonsai-ists in serious long term studies, experiments, arguments, etc., and they long ago came to terms with some of these (rather basic) things and long ago stopped trying to reinvent the wheel. There are hundreds, thousands of renowned and highly educated scientists, gardeners, etc. who have gone very deeply into research on these subjects and instead of beating their heads against brick walls ad infinitum, have accepted what (practically) can't be changed and gone on to spend their energy and talents on other things. I know you 'know what you know', but it's a big pond out there, and perhaps you might want to either do a lot more reading (if only to realize what a thankless 'job' you're undertaking, and/or stop beating dead horses (I'm a great one for cliches tonight!) and just enjoy growing what is doable now - bonsai's such a big issue anyway, with plenty to keep you busy forever, why fiddle around trying to disprove 2+2? Of course philosophical ideas (ideals) should always be questioned, but these are old, known, proven scientific facts!

Lucy
I couldn't disagree with you more here. When you mention this subject, were you refering to root rot and the technique to save trees affected by root rot. My experience with maples is not consistent with what you claim; I have had 20% success rate with maples.
I would like readers to test this claim out when you get a case of early(emphasis on this point) root rot. Chop off the main trunk as low as possible but preferably leaving one or two branches. Without doing anything else, you will be amazed that the tree may overcome the rot, recover and grow into a healthy tree. Reducing transpiration immediately assists the plant to balance water loss and osmotic intake. That is all that is required to save the bad situation.
These old proven scientific facts, you would like to claim as empirical and there is no point in reinventing the wheel, to use your cliche. Sorry to point out that some so called facts have been proven to be wrong as Science advances. Maybe this link may help:

http://www.copernican-series.com/sss/

Hi, I wasn't referring to rot, but to trying to grow maples in the tropics (for instance). Of course science advances, but until something really radical takes place in the world to the extent that basic characteristics of organisms change 360°, and mainstream science acknowledges it, I wouldn't personally invest a lot of my time or energy in pursuing such an idea. I've worked with scientists most of my life, and am well aware of possibilities... and (until proven otherwise) impossibilities.

Thanks Lucy,
I now get the gist of your wavelengths. I also like the darker or less traveled side of a coin. I am aware of the impossibility of the quest and agree that it is foolish to expand precious time and energy chasing a dream.
I have been a rebel all my life and at this stage, not likely to change my spots, call me stubborn,even obstinate; fits me like a tee.
Know what. I believe I have still lots of time and energy left to search for the impossible dream, maybe I have become a virtual dreamer. Anyway it is a good thing that is not a crime. To each his own then and peace be with you.

Sunshine, Flip a coin and then take the path. Either way, the odds of saving the tree are slim.
From what I have read and experienced by growing plants and education in college, I would have to lean toward to pruning the foilage back.
Root rot has has nothing to do with wet roots, it has to do with fungus/parasites living in the roots. Keeping the roots wet promote the likly hood of getting root rot, but the two are not interchangeable.

Go down to home depot, lowes or where ever. Go to the garden section, buy a juniper there in a one gallon container. Down here in the south you should still have a good pick of trees. Go over to the pond section, buy a bag of profile aquatic, thats your soil, dont mix it with anything. Here in the south its hot enough to use that as soil by its self. Then find a nice bonsai pot somewhere, youll probably have to go to another store.
The sooner you do the above, the sooner you getover your other tree. Just remember, water only when the soil is dry. Junipers can handle drying out the soil completly for a few days.

I hope this got back to the orginal subject and helps you out.

jamkh and Lucy, I love reading your stuff but you both realy went off on tangents here. Just a helping hand stearing you back... lol...

The voice of reason :-)!

Bill
Your advice to Sunshine avoids all the indigestion. Thanks for steering us back to reality.