When Andy went to retrieve the orders he was discovered by John Hammond in the buttery, John who was stealing wine himself and running the spice racket was not best pleased to find Andy there. Andy suspected John had the orders as they were not where they should have been, and so tried to retrieve them and ended up killing him as John started to make a disturbance. He then searched the body but was unable to locate them. He decided to get rid of the body by throwing it over the castle walls, planning to move it later on, on Saturday to a quieter location. However he hadn't reckoned on Ade the huntsman going on an early morning walk looking for deer. John was obviously not killed in the fall, being dead already from a stab wound to the heart.
When the body was discovered Andy decided to incriminate someone, it didn't matter who really, just as long as his cover wasn't blown before he completed his mission, which was yet to be finalised.
Now Andy had a problem, he had to try to find the orders he was due from Richard Gloucester, he was fairly sure they were going to be important ones, but he needs to see them. He eventually found out on the Saturday that Jock the Captain had being quizzing Kyle Glover about who the letter was for that he dropped off in the buttery, and realises that if Jock works out who the orders are for he could be in big trouble, so decided to eliminate Jock, as Jock no doubt has the orders he needs, and who was after all was a nasty piece of work.
On the Sunday Stanley turned up after having been summoned home by Lady Joan his wife, he was needless to say not best pleased when he turned up to find not only was Margaret Beaufort there stirring things up but Sir Richard Brown had arrived to take over the castle, his daughter had decided to develop an interest in men, the servants were up in arms about thieving and to top it all off there are 2 dead men, one of whom was his staff the other the Gloucester Captain Jock, with the murderer still being loose in the castle. And rather than being able to put his feet up after a hard ride back from Northumbria he was expected to sort it all out.
The start of the investigation was to establish what had happened on the Saturday and to decide if the accused was in fact guilty of John Hammonds murder. Mark Hewitt the surgeon thought that the two murders were sufficiently similar as to be by the same person, the stab wounds were similar in size and placement. But if a small person had killed John Hammond they were unlikely to have been able to have carried him to the castle walls unaided. This cast doubt to the validity of the conviction on Saturday, as the murder of Jock happened when Johns suspected murderer was being tried. Jock was a nasty piece of work, there didn't really seem to be any one foolish enough to take him on. Stanley came to the conclusion that Jock must have known the murderer and was surprised by them. There is also the possibility that Jocks murder was a copy cat murder.
The obvious suspects were Nigel Lamb, who was the Captain in charge of the castle guard, they didn't see eye to eye on anything, Mary who while being small could have stabbed him, Jock did seem to have issues with her about money, Kyle Glover as Jock bullied him mercilessly. Fran Wood as he seems to be jealous over the attention Jock was paying Laura. Rebecca also argued with Jock about her sister Mary. James was also known to have a grudge against Jock, he felt that he had been passed over and should have been the Captain.
On a slightly less important note Stanley needs to find out what was going on with the spices and wine, who was John Hammonds accomplice, maybe they murdered him. The cook, Rachel Beasley must know what is going on, so Stanley gave her a hard time, after all this is why he didn't really want her staying on after her husband had died. One consideration was that maybe the cook murdered Hammond, either for a bigger share in the spice stealing, or to stop it.
The politics are exactly as they appear, Margaret Beaufort was recruiting both money and support from local wealthy families in order to put her son Henry Tudor on the throne, and also trying to gain the support of the Stanley family, after discovering that marrying in to them wasn't enough to buy their help. Fran Perry was sent to negotiate on the families behalf, whist Chris was there due to his money and far reaching connections on the continent and throughout England.
Andy's orders from Richard Gloucester himself (the letter delivered by Kyle) were to find out what Margaret was up to and if possible assassinate her. She is of course a well known trouble maker. Being that Jock found out this he definitely needed to be removed before he had time to work out who the orders were for and either blackmail him or incriminate Richard Gloucester.
Unbeknown to Andy there was another spy in the castle, acting for Margaret Beaufort. This was Susanne who used her children to gather information and had seen Andy acting suspiciously. She suspected he was a spy, but not what his purpose was, and was waiting to gather more intelligence and possibly find something to incriminate the Gloucester faction.
In summary, Andy Horsfield murdered John Hammond simply because he was in the wrong place at the wrong time and also murdered Jock as he discovered he was a spy and had orders to assassinate Margaret Beaufort.