(Capcom's primary storyline)
When the t-Virus outbreak occurred, all of the staff working on the estate, including Martin, became infected. During the early stages of infection, Martin attempted to slow down its progression, but was only able to halt the infection for a few days. Martin later went back to his room, as the estate became too dangerous to walk around in, due to the numerous zombies that were wandering the halls at that point.
In his last hours, he wrote his will; a letter to his significant other, Alma. In his letter, he told about the events of the t-Virus outbreak, the effects of the virus and what it does to the mind and how it turns its victims into mindless walking corpses that feel no pain or emotion. By this point some of Martin's reanimated colleagues had located his room and were mindlessly banging against his door. He also apologized for not calling her earlier, citing that he was forbidden to make outbound calls by Albert Wesker (whom he only identified as a man wearing sunglasses).
As the infection progressively got worse, he started suffering from advanced stages of memory loss and became very aware that he was forgetting more about Alma by the hour. Knowing what the infection would do to him, Martin decided to end his life before he lost what was left of his sanity.
Days later, when the surviving S.T.A.R.S. Alpha team members were investigating Umbrella facility, they discovered Cluckholm's will in his office. Curiously, his body was not in his office, suggesting that he resurrected and likely found a way out of the office.
In Jill's scenario, the top portion of the letter was torn off, presumably by either Wesker himself or Barry Burton from Wesker's manipulations, in order to remove incriminating evidence towards Wesker's ties to Umbrella.