I checked “The Ionian Mission” last night, and it is the “by and large” incident in that book. The Worcester was transporting a number of parsons to the Toulon blockade, (including Professor Graham and Mr. Martin), much to Jack’s dismay. On the way there, they were involved in a small battle, during which Stephen was the only injury. Each parson thought it his duty to visit with Stephen, much to his dismay. He found Graham to be the least objectionable of the lot. But during one of Graham’s visits, he saw fit to insult the mental abilities of Naval officers, which annoyed Stephen, leading him to defend the great complexity of sailing ships and the knowledge required to sail them. During this, the following exchange occurred:
“Such tales have I heard of Captain Bentinck’s palls, or rather shrouds, and his triangular courses, of Captain Pakenham’s newly-discovered rudder, of Captain Bolton’s jury-mast, of improved iron-horses, dogs, dolphins, mouses - or mice as some say - puddings…”
“Puddings my dear sir?” cried Graham.
“Puddings. We trice em athwart the starboard gumbrils, when sailing by and large.”
“The starboard gumbrils…by and large” said Graham, and with a passing qualm Stephen recalled that the Professor had an unusually good memory, could quote long passages, naming the volume, chapter, and even page from which they came.
Then at dinner, while Jack was admiring a spotted dog, Professor Graham asked about the phrase, and the officers basically told him it was nonsense. Gumbrils don’t exist, and sailing “by and large” is impossible:
With a piece of fresh Gibraltar bread and arrows drawn with wine he showed the ship lying as close as possible to the breeze: “…and this is sailing by the wind, or as sailors say in their jargon, on a bowline; whereas large is when it blows not indeed quite from behind but say over the quarter, like this.”
“Far enough abaft the beam that the studdingsails will set,” said Whiting.
“So as you see,” continued Harris, “it is quite impossible to sail both by and large at the same time. It is a contradiction in terms.” The expression pleased him, and he repeated, “A contradiction in terms.”
Graham was offended, and insulted Stephen a few minutes later. They didn’t speak again until Graham left the ship. Stephen was sorry that he offended Graham due to his offhand remark, but honestly never expected to see him again.
The only reason Graham showed up again was because Stephen had been put ashore in France to attend a secret meeting of various French agents. He was unaware that Graham was also attending the meeting, although he knew Graham was probably a member of a rival intelligence organization, since he had tried to recruit Stephen. The meeting went bad before anyone even arrived, and Graham accidently shot himself in the foot. Stephen found him and brought him back to the ship, at which point Graham pretty much had to forgive him, both because he was revealed as a fellow (and superior) intelligence agent, and because Stephen saved his life.
Oh, and the bear incident? Absolutely they thought he was real bear. “A led bear knows how to dance. 'Zis is logic.” Stephen had gotten advance notice that all British subjects were going to be arrested, so he & Jack (in the suit) headed south ahead of time. They just happened to come across a detail of French soldiers leading British prisoners to prison. The only reason the French soldier made him dance was to impress one of the female prisoners. But none of those soldiers were searching for Jack specifically (if anyone was).