We're very excited.

So Minnesota Republican Representative Michele Bachmann told the Washington Post, commenting on the shutdown that ground many critical government functions to a halt for over two weeks. "It's exactly what we wanted, and we got it."

So, what exactly did Bachmann and her Republican colleagues get out of it? A lot more than they may have bargained for, according to scientists employed by the federal government. It is not just that government researchers were locked out of their labs and offices, but whole programs were wastefully delayed and, in some cases, endangered.

I talked to Tom Greene, an astrophysicist at Nasa Ames research center outside of San Francisco. Greene is working on the James Webb Space Telescope – the eagerly awaited successor of the Hubble, with even more power to peer into heretofore unseen reaches of the universe. He told me that more than 100 scientists had gathered from all over the world to conduct critical equipment tests in preparation for the launch. But that all ended on 1 October when the government stopped writing checks.

Not only did this delay cost the program an estimated $1m a day, but, given Nasa's tight schedule, some tests may never get done now. This "is kind of scary", Greene says, given the immense complexity of the world's most powerful telescope.

This is only one of untold thousands of projects that were mothballed when Congress's failure to approve a budget defunded the US government at the start of the month. Federal websites were taken offline, scientists couldn't receive emails, attend meetings, or interact with their colleagues. Crucial environmental, food safety and climate monitoring programs were either suspended, or substantially scaled back.

Now that the whole bizarre episode appears to be over, it's a good time to look at what it cost American taxpayers – and the science which we collectively support. Where to start? Let's begin as far away from Washington as we can get – in, say, Antarctica.

The National Science Foundation, which is funded by the federal government, had to send the scientists home during key field season and shut down projects ranging from climate research to studies of penguins. Will they return now that government funding has been restored? Well, maybe not. "Some activities cannot be restarted once seasonally dependent windows for research and operations have passed," the National Science Foundation cautioned in a statement. Oops: so some projects may have just blown a whole year's research.

And speaking of Antarctica, a US delegation had to suspend its trip to Australia, where representatives of many nations are gathering in hopes of agreeing on the creation of the world's largest marine sanctuary. America has been one of the most enthusiastic proponents of this; Russia, which has fishing rights in the area, has resisted.

The meeting starts in a few days. So, with any luck, there might still be time to book the flight. Would it be too much to ask the Republicans in Congress who caused the shutdown to chip in for late booking fees on those tickets?

Closer to home, there are the lab animals that were being used in research on diseases like diabetes, cancer and Alzheimer's. National Public Radio reported that thousands may have already died or been killed by researchers who could no longer maintain them, including colonies of genetically altered mice that are unable to survive without constant monitoring by scientists. To revive these unique strains now will be costly, both in time and money.

Andrew Rosenberg, the director of the Union of Concerned Scientists' center for science and democracy, has been looking into the impact of the shutdown on researchers around the country. He told me about a wildlife biologist who tags grey wolves who just missed the heart of his yearly field season; a researcher monitoring currents in the mid-Atlantic who couldn't get access to his ocean site during a recent tropical storm, which he had been waiting for all year; a cancer trial that had to be cancelled; students who lost critical training time … the list goes on. Rosenberg says:

It's not just that people go home for a couple of weeks, and then everything gets back to normal and they go back to work. These things have a long term impact.

I asked him about direct federal funding of science – which has been hit hard by the sequester and other budget cuts in recent years – and just how important it is.

"It's not just the funding stream … it's the data set," Rosenberg replied. He is referring to the fact that the federal government is the repository of what may well be the largest trove of scientific information on the planet, on which scientists all over the world depend. When this tap gets turned off, research in many fields slows to a crawl. Rosenberg elaborated:

It is all so interconnected now. Federal researchers collect data that is utilized by researchers in academia, by people working in industry, at state and local levels, so when you ask how dependent are we on the federal government in terms of science, it's a bit like asking: do you need your left leg?

For now, at least, that left leg has been restored, and scientists in the US and beyond are breathing a sigh of relief. Yet, for many federally funded programs, irretrievable damage has already been done.