It is, of course, impossible to know what he was actually thinking, and Hess did not explain his motivations in his suicide note, but some guesses can be made.

Here is a previous answer I wrote where I go into more detail about Hess' incarceration - you might find that interesting.

By 1987, Hess had been the solitary inmate of Spandau prison for 21 years. Attempts to have him freed were stymied by Soviet insistence on keeping him incarcerated (both for propagandistic reasons and also so that they could maintain their foothold in West Berlin), and plans to move him somewhere less expensive to maintain never got anywhere. Hess' family was very active in the campaign to get him freed, and Hess himself communicated quite a bit with them through prison staff, who smuggled letters for him, so he was kept well-informed about how the campaign was going. When Gorbachev came to power in the USSR it resulted in hopes that maybe he would allow Hess to be released, but there was no sign of that. On top of that, in 1987, Hess' health began to decline. Thus, it seems likely that he killed himself out of desperation, knowing that his death was already looming and he would never be freed.

Source: 'Tales from Spandau' by Norman Goda