Another year in the life of Diddly Squat Farm, run by Jeremy Clarkson, Britain's best-known but least-qualified amateur farmer. Season 2 of Clarkson’s Farm promises to be even better than the first as Clarkson and his rag tag group combat the public, the council, and the government.
In the first episode, Clarkson attempts to diversify his farm's revenue sources (having made only £144 in the previous year) in an effort to increase his profits. He decides that his primary way of doing this will be a new herd of cows and promptly purchases several of the animals. However, the timing of when they will bring in money and the necessity of building an enclosure for them causes problems for Jeremy and Charlie. Meanwhile, inspired by the success of the farm shop, Clarkson has the idea to open a restaurant in the abandoned lambing barn to sell his beef and lamb, but he must deal with the cost of converting the barn and getting approval from the local council.

Clarkson's herd of cows begins to settle in on the farm, but things immediately begin to go awry. The cows aren't keen on the idea of a fence and quickly escape, and when Clarkson attempts to wean the calves, they too break out and cause chaos. In addition, the new roosters brought in to help fertilize the soil also prove to be difficult to handle.

Clarkson is ready to submit his application for his farm restaurant; he must use gentle navigation and respect for bureaucracy in order to keep his interests afloat. This, of course, is not easy for Jeremy, so he must be careful. Faced with Council powers that be, Jeremy uses two of his greatest skills: diplomacy and respect for red tape.

Jeremy comes face to face with his nemesis: the badger. Clarkson is informed by Charlie that his cows are in danger of contracting Bovine Tuberculosis from the badgers on the farm. He decides to resolve the issue by killing the creatures but is informed that this is illegal in most cases. Faced with a danger to his herd, Clarkson must hope for the best.

The results of the TB test are in... but just as important is the fact that numerous calves are scheduled to be born in the next couple of weeks. The first few happen very quickly in the dead of night before Jeremy's woken up, but soon he and Kaleb are dealing with some very challenging situations. Jeremy also meets local farmers to discuss a farmers' co-operative to supply the restaurant - much-needed by some who are really struggling - because the clock is counting down to Decision Day, when the Council will hold a public meeting to decide the fate of Jeremy's restaurant.
After weeks of waiting, the day of judgement for Clarkson's restaurant is at last here. He and Charlie set off to put their case to the powers that be. Is it a Yes? Or is it a No?

Everyone's still reeling from the council's decision and its implications: the money Jeremy's spent on cows for the restaurant, the locals who won't find work there now and the farmers' co-operative that's now defunct. Charlie sets out to find a legal team to help Jeremy appeal the decision, as Jeremy and Kaleb get to work on tagging the new calves and attempting to navigate a government helpline where you're supposed to register them.
There are other useful distractions from the council in the shape of Diddly Squat's Hedge Laying Competition and a mouse that brings the whole farm to a standstill. The legal team that Charlie has assembled pay a visit. They outline their strategy for the appeal, but also the costs that come with it.