The first one. All cells must come from pre-existing cells.
Pasteur did the experiment to show that life was not spontaneous. By boiling the media in the flask and not letting new microbes in (hence the swan neck flask), enough air could get in, but not microbes.
He proved this by tipping the media from the flask into the swan neck and then letting it go back into the main part of the flask. A few days later - contaminated. So by picking up a few microbes that had managed to get into the neck area, he was able to get reproduction...but not without doing that!