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When we were faced with our first cadaver, smelling partly of formaldehyde and stinking partly of rot, because it had not been well preserved, we all held our noses and plunged in, covering for the students who were in the lavatory throwing up.

Dose the whole sentence in bold mean: we quickly fled into the lavatory and vomited up in turn?

Source: Listening for Lions by Gloria Whelan

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Does the whole sentence in bold mean we quickly fled into the lavatory and vomited up in turn?

No, it does not mean that. And you are erroneously thinking of the two different clauses as one sentence (note the separation by the comma). It is a little difficult to make sense of what is going on without more context, particularly without knowing how those identifying as "we" are different from the rest of the class.

Let's assume "we" is referring to person A and person B.

When A and B encountered their first cadaver, they instantly started working on it, despite the bad smell and all that. But why?

we all held our noses and plunged in,

"Plunge in" is a phrasal verb meaning "to suddenly start doing something actively or enthusiastically."

Now the question is, Why did A and B plunge in? Why didn't they just stand around and watch what others did? The answer is here in the last clause:

covering for the students who were in the lavatory throwing up

Other (or some) students in the class were in the toilet throwing up due to the bad smell. And it was perhaps their turn to work on the cadaver. So, while they were throwing up, A and B stepped in to cover for them.

"Cover" here means "to do someone else's job or duty when they are absent."

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