The most talked of attack on Castle Heterodyne was the one that started war with The Other. Supposedly carried out by The Other itself, the massive explosion severely damaged the Castle, severing the main intelligence from its subsystems and causing major structural damage.
The attack claimed the lives of 63 of the Castle's 207 staff members, including the new seneschal (son of Carson von Mekkhan) and the infant Klaus Barry Heterodyne. Afterwards, the Lady Lucrezia was found to be missing, her notes burnt, and her assistants murdered.
Barry organized the clean up, and the day after the attack he and his brother left to look for Lucrezia and fight The Other. As far as anyone knows, they never came back to Mechanicsburg, leaving the Castle badly wrecked.
Following Agatha's arrival in Mechanicsburg, the Castle was once again under assault, by both The Storm King conspiracy, who covertly constructed a device to kill the Castle's intellect, and Baron Klaus Wulfenbach, who planned to launch a full frontal assault and physically smash the structure. With Agatha and her friends and minions' help, these attacks were repelled and the Castle regained its facilities, both mental and physical, driving all of the attackers from Mechanicsburg.
It is noted in the Girl Genius print novels that the attack on the Castle did not follow the Other's usual later tactics, namely the dropping upon the target of the moment from a great height both slaver wasp swarms and big heavy rocks.