In this case, "extra" refers to a special edition of the newspaper produced particularly to cover breaking news.

In the 19th and 20th centuries, major metropolitan newspapers would keep a particular publishing schedule. Most would publish a new issue daily, either in the morning or the evening. Smaller towns might publish once per week or several times per week, rather than daily.

Within their schedule, the largest metropolitan newspapers would publish several editions throughout the day (and this practice continues to some degree in various places). The first edition would be the one bound for locations farthest from the printing press, while a metro or late/final edition would be intended for audiences closer to the press.

Extra can apply to both an edition or an issue. It can be an extra edition published after the final edition, something issued because of late-breaking news, or it can be an extra issue published at, say, midday or (in the case of a weekly newspaper) on a date it would not normally publish.