I suspect they worked for a different 3 letter agency and just were borrowing the letters D, O, and E.

yep, and measuring something far more interesting than radiation levels.

I can't imagine something more interesting than radiation levels. Video? Boring. Audio? Even more boring. Maybe WiFi or other radio signals? Still radiation is much more interesting then those mundane things.

My guess is that Paul and Matthew were building something like a stealth Geiger counter.

The secret project doesn't seem to be a stealth Geiger counter. The custom iPod they created had complex data recording and storing features, excessive for a Geiger counter. The device was probably made to intercept WiFi data, which makes more sense to secretly record.

Why not start with a device that already has WiFi, and then you don't need to do any hardware mods?

I suppose using a device that's known to not have WiFi would arise less suspicions

Although I believe it's common practice in secure installations to CT scan everything in and out.

No hardware mods are a much better way to not have evidence sitting in those CT scans.

Back in 2004, this kind of thing could have just been a favour.

Now, apple collaborating to add spy devices could seriously hurt their privacy reputation. I wonder if things like this still happen, and what persuasion executives require to enable it?

Hobbyists enjoyed getting Linux to run on iPods, which was hard to do without the special knowledge and tools Apple possessed. We on the iPod engineering team were impressed. But Apple corporate didn’t like it. Starting with the iPod nano, the operating system was signed with a digital signature to block the Linux hackers (and others).

I'd like to know exactly why they were opposed to this, given that this was way before the App Store was a thing and there's nothing to protect otherwise.

It's not a cover for a 3 letter agency, Energy IS a three letter agency.

Most people don't actually know what DOE is. For starters, it's officially one of the 17 USG intelligence agencies.

It houses the national nuclear security administration which is responsible for military reactors, nuclear weapons, and nonproliferation.

It operates the DOE Science and NNSA Weapons national lab and site complexes via M&O contracts (of which Bechtel is one of the longest contract holders).

NNSA is congressionally funded via energy and water, but it's authorization is via the armed service committee National Defense Authorization Act (same as the military).

None of this is a nefarious secret, and all of this and quite a bit more can be found via the agencies website.

Folks completely misunderstanding what government does. Forget about DOE, how many folks actually understand what HHS does, or HUD, or any of the dozens of other agencies other than Defense and State.

The USG is full of these enormous and powerful bureaucratic orgs. Not surprised that most folks (including me!) Are unaware of what our tax dollars fund, but boy is it a lesson in complex systems.