Short term: my advice is to be very aggressive with your career management.

For better or worse, your career history is judge on how successful the companies you worked for.

Ask yourself, knowing nothing, which engineer would you hire:

Engineer 1-- did engineering on the Uber app

or

Engineer 2-- did engineering on Yadzoks, the leading shovel sharing app (shut down after 13 months, being unable to raise series A)

Could be that Engineer 1 was a bump on a log, and Engineer 2 was a total champion. But truth is Engineer 1 gets more love, probably out people's suppressed fear of the randomness of software market success and the irrational belief that maybe Engineer 1 "knows the answer" on how to be successful.

So you have the equivalent of a "dud" on your cv. Probably no worse then a random VC backed software flame out, maybe you'll get a few "har hars" at the beginning of the interviews, but most hiring managers will think they have you at an advantage-- was this guy just coding an internal wardrobe app for Elizabeth Holms? and not working on cutting edge, successful products?

1) Your best bet is to go quickly... you'd rather be the 1st engineer out, rather than the 500th.

2) Because hiring managers think they have you at an advantage, be humble, give them 1 (and only 1!!) piece of dirt where it seemed like something was amiss to acknowledge that you worked at a dud.

3) Don't "hold out" for the right position. If you get the dream job take it, but even if you don't if you think its a decent role and something you can build on it, take it. You're best to view this as a 2 year step back: take something more junior, with lower comp, then kick ass, prove yourself, get the step up in 1 year, and if they don't then look again for your ideal position. You'll gone a long way to "laundering your experience"

As a general rule, it is best to be brief and factual about any negative issues and move on. Avoiding them makes people suspicious. Staying on topic suggests that you are nervous and might have something to cover up. So be to the point and move on.

Good luck with your job hunt.

Theranos problems rest solely on the shoulders of its leadership. Any reasonable hiring manager will understand that there will be some exceptional rank & file staff coming out of there. (Ex: Arthur Andersen/Enron) Your role was far too junior to be caught up in the shenanigans.

Incidentally, be sure to quietly line up individual supervisors and colleagues who can serve as professional references.

So, be prepared to field questions like "Did you know about the unethical $STUFF going on?" and "How could you not have known about $STUFF?" etc. You might even get interviews that you otherwise wouldn't just so they can satisfy their curiosity and ask you that sort of question. Milk it where possible.

Anyway, unless you were upper management, none of the stink should stick and create a problem for you (unlike other spectacular flameouts where the ethical problems were widespread throughout the organization).

The morality and ethics of Theranos are in question, not the quality of their software, most organisations would be more than happy to have a former Theranos engineer in their ranks.

No one thinks the engineers are the liars or frauds, it would be really hard for a company to corrupt all the engineers on that scale without the whistle being blown much sooner that it was - employers will know that.

Stop worrying and go find a great place to work (preferably somewhere a little less controversial.... Uber perhaps!).

I have a hard time seeing it making any difference either way.

Don't get nervous at a problem that doesn't even exist yet.