[Rainbow Six]

Possibly, but possibly not...it partly depends on one's interpretation of the Strategic Defence Review at the end of the Cold War (aka Options for Change) and what effect it might have had. Prior to Options Fishery Protection was handled by Royal Navy patrol ships based out of Rosyth.

Out of the big three Navy bases in the UK at the time (Rosyth, Portsmouth, and Plymouth) Rosyth was generally perceived to be the biggest loser of the Cold War drawdown with many of its tasks being transferred to the two English bases during the start of the 90's. We've already mentioned the nuclear sub refitting in another thread; the Fishery Protection Squadron ended up in Portsmouth. Marine Scotland (as they now call themselves I believe) took over the task in the mid 1990's.

However it's possible, certainly in a V1 timeline, that Rosyth would have remained on an equal footing with the other two bases, so might have retained the Fishery Protection Squadron. Probably less likely in V2.

To be honest, an intact Rosyth (it wasn't on the canon target lists and is far enough from Edinburgh and Grangemouth to avoid any serious damage) is one reason why I find the situation in Scotland described in the Survivor's Guide to the United Kingdom somewhat...implausible. At the very minimum an intact Rosyth, together with RAF Pitreavie Castle (closed in 1996 IRL) which was just a couple of miles down the road, should have enabled HMG to maintain a decent presence in the area imho.