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This is the second time that my baby girl has been severely ill. While I am left feeling quite ashamed, I prefer to share the lesson-learned over kicking myself. The vet never really figured out why/how she got sick last time. This time it was almost a no-brainer: poor water quality that allowed algae growth on her shell that went untreated.
Cause of poor water that got the ball rolling: going on vacation leaving her in the care of teens whose solution to a clogged filter was to simply unplug it. We came home to one nasty tank (that was in July). We did a partial water change and let the filter do the rest of the work. Obviously, that was not enough. Instead, we fostered a perfect little environment for dark algae growth on her shell.
Penelope started to shed her scutes in August even though she had already done so in February (hint #1). I felt it was odd, but not enough to set off any alarms. Penelope was acting fine, so I just gathered them up, tossed them on a paper towel to dry and then tossed them in a jar. When they were wet, nothing stood out. When they were dry I didn’t think to check them out.
Now that I learned why Penelope wound up with sepsis, I went back and looked at all the scutes and can clearly see the progression. Total time from algae invasion to sepsis = 4 months.
Algae:

Sepsis:
This was a tricky one. Please remember, when you live / look at something every day you don’t really notice gradual changes – liken it to someone you see every day going bald; you simply don’t “see it.” What caught my attention was when the webbing of her feet started turning pink. I couldn’t deny that. All of a sudden Penelope stopped eating and I took her to the vet.

When the vet looked her over and pulled off some loose scutes, the bubble-gum-pink hue shocked me. Not much to say about that. She also pointed out indicators of an unhealthy shed.

Treatment for the algae: Dry docked for 3 weeks at 80 degrees or higher and Betadine soaks with toothbrush rub every other day.
Treatment for sepsis: Two antibiotics (one taken every other day, and one daily). My vet was kind enough to put them in a bacon flavored suspension so I wouldn’t have to battle trying to give shots to an 11” grumpy turtle.
Lessons Learned: 1) Take a few seconds and look for algae every now and then; 2) Take a peek at those shed scutes once they have dried; 3) good water quality is more than just having sparkling water; 4) if you think your little guy or gal is turning pink – have someone who doesn’t see them every day take a look; 5) vet, vet, vet, vet…
Vet Cost:
Yes - vets cost money. After Penelope’s last round of illness, I started a “Penelope” fund in case I ever had to go to the vet again (glad I did). Every payday I drop a few bucks in. This time I told the vet exactly how much I could afford, so she bypassed the tests and went straight to the antibiotics. Not the preferred route, but at least one I could afford.
If my major lameness helps someone else keep their RES in good health, then it is worth airing my dirty laundry.

Sorry to hear about the difficulties. Did your vet make a sepsis diagnosis from the light pinkish color on the webbing? It's something I've observed on my RES and others (especially older ones), but there are no symptoms to suggest sepsis. Her shedding is still far better than dealing with fungus... it makes such a terrible mess.

I think your "lessons" and "fund" are a great idea, everyone should do the same or something similar.

Actually, the webbing is what made *me* sit up and think.
The vet based her diagnosis on a combination of things - Penelope's skin on her rear end and under her neck had a pepto-bismol / bubble gum pink hue. She found the same pinkish hue on her carapace when she pulled off some of the loose scutes.
We have a return vet visit in 2 weeks, I'll ask the vet about the webbing. Knowledge is power.
I must say Penelope is looking much better - still not eating, but her shell looks like shiny and polished even when its dry

Question on Habitat Clean Up:
I ordered new media for her filter and when it arrives I'll be doing an overhaul on the tank. I can't think anything else special to do except scrub it down with a clean rag and super hot water. Any other suggestions?
I'm hoping the media arrives soon, so the tank cycles before its time for her to go back in (I've yet to do a complete water / media change without the ammonia and nitrates sky rocketing). I ordered some ammonia-zorb hoping it helps...again, any suggestions are appreciated.

Regarding the light pinkish color... I also notice it where the skin meets the shell. It's better to be cautious, but I've always understood it to be the norm in older RES.

Don't use hot water cleaning the tank... it can crack and it's happened to a member before (I think Starchick). Just drain it and use vinegar. Air drying will also be good. As for what media to use, check out this topic and locate your filter: viewtopic.php?f=9&t=30145

Whew! After nearly three weeks, she has stopped hiding under the towels in her dry-dock home. The same day that she came out from under the covers, she finally ate something! While not a great staple, I offered some tuna (packed in water). At this point any food is good in my book. She's not going for her pellets, so I'm going to soak some in "tuna juice" and see if she goes for it.

She less grumpy (not trying to bite off my finger when I come near her) and the Betadine soaks have done wonders on her shell.

I'm telling you - if you have a large RES, try talking your vet into providing a suspension liquid to administer medication. Even though administering it is a two-person job, it beats trying to give injections hands down!
Thank goodness I had my "Penelope Fund" - As mentioned before, I set aside a few bucks each paycheck, and it DEFINITELY was worth it!
If it weren't for my vet Penelope could have, and probably would have, died. So let your pennies stack up; it is worth it!!!!!
We have a follow up appointment on Tuesday - hoping for good news

Thanks for the update. Poor girl must be pretty stressed! Good point about the medication too and I would try the oral form first. Did you actually use a soak, scrub or both?

Soak and scrub with a soft toothbrush.

I'm interested in learning more about the algae. I was concerned about algae growth in Oliver's tank a few years ago. When I read around this site, though, it seemed to me that most people were saying algae is pretty much inevitable even in a clean tank, and not worth worrying about. So I stopped worrying about it. Is it a certain type of algae that was the problem for Penelope? If so, how do you recognize it? Or is all algae growth a problem?

In this particular case, it was brown algae. I'm going to the vet tomorrow, so I'll ask her for details and post the response. I don't want to confuse people...

Aha! These pictures provide a much accurate reflection of what I was trying to describe above when talking about the bubble-gum pink rear end and pink-tinged shell that helped lead to her diagnosis.
Maybe I should delete the ones above since they look more orange than pink (?)(?)
These aren't my guys, but the look is exact!

She's got her dancing shoes on! Here she is - bone dry - and all ready for the trip to the vet.

The pink in that other set does look worrisome. Penelope looks great, I'm glad she's doing better.

Update: She was doing well (ate for four days in a row), bright eyed and moving around. She still has some pink on the underside of her neck, so two more weeks of antibiotics; sadly the water change in her tank cause the ammonia to skyrocket ( no surprise). The vet was very clear about not putting Penelope in the tank while the ammonia and nitrate levels of are up, since Penelope is on the mend. So that meant that Penelope had to get her water break in a small bin - just what she needed, more stress. Anyway, she stopped eating again. All along, she has been moving towels around and hiding under them, except last night...she stayed in one position all night. Something was odd, so I kept checking in, and each time she was still sitting there with her eyes open and they were getting puffy. This morning I did a partial water change to lower the water level and put some warm water in to make sure it was above 80 degrees (not something I would normally do, but all things considered I wanted her in her tank, not a bucket). I took advantage of that small window between partial water change and rising ammonia. When I put her in, she sunk straight to the bottom without moving her position. Finally, she swam across the tank and popped her head up for air. I had to keep an eye on her to make sure she could swim up for air. She made it up,but had to push off items in the tank to get there. Then she balanced herself on the water heater and stopped moving. She has seriously declined. The largest hint of all was when I went to remove her from the tank for her dry docking. Usually it's a big chase and she comes out kicking...today she just laid there - no fight at all. Gave her the antibiotics and put her in "bed" - since then, she has extended her neck a little and lying with it kind of sideways. No movement except blinking her eyes...at the moment there is nothing I can do. She has her medication, is dry-docked, warm, got to swim, was offered food, and has a "towel tunnel" where she can get away from the lights if she chooses. So I am just letting nature take its course and hoping all this worry turns out to be for nothing.
And, yes. I will be calling the vet first thing in the morning.

Hopefully, it's just a bit of the stress and the unusual routine thats got her down. When she sunk to to bottom, how long did she stay there?

She stayed there for about five minutes, went to the top took a breathe and went back to the bottom again. Other than when she was swimming to the top for air, she had/does have all her limbs tucked in. Weird thing is I dropped a small piece of tuna in. It basically, landed right on her nose and she seemed to eat it, but didn't move to get it (just a lucky shot, I guess). I dropped a few more little pieces in - aiming right for her. They missed, and she made no attempt to eat them.

I just checked on her and she has actually moved about three inches to the right!!!
Wondering if I should cover her up, since she has basically been under the basking lights for 24 hours or more. As I mentioned before, normally she would tuck herself under a towel to get away from the lights...I just don't know if she is out because she wants to be, or if she is out because she doesn't have enough umph to get under the towel...