I have reviewed my 2 posts on this thread and find no error with them. And as Fare-Cop has clarified, it already has gone to Court - it is a Summons to attend Court issued by the Court. I stand by my assessment.
If it helps to inform your judgement, my posts are based on more knowledge and experience in English and Scottish Courts than a solitary civil action for the collection of a personal debt.
I have more experience of the courts than that too (industrial tribunals, county court, currently involved in late stages of negotiations in civil proceedings). My personal experience of the magistrates court is limited to a single summons to attend Court, issued by the Court, which I had withdrawn.
I have not claimed exhaustive knowledge but I pointed out, and I stand by my assessment, that the OP should do what he can to get the summons withdrawn, as a matter of indisputable and unarguable common sense.
I repeat, that the Railway Operator might be persuaded to withdraw the case from the bundle listed on that day, but the grounds for doing so would have to be substantially more persuasive than those posted here by tobymcg.
I wouldn't presume to determine what they might find persuasive.
The OP should take whatever steps he can to get the case withdrawn. There is no guarantee that he will succeed, but rather than advising that it is a fait accompli and saying that it is too late, which doesn't achieve anything, he needs to address this matter now.
If he has not already contacted FCC by this point today to seriously settle this (and without complaining about their service) then he is not taking this seriously enough.
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Whilst I usually agree with most of your posts, I think this piece is a bit confusing. The OP tells us he has received a summons so the matter is already with the Court.
He may still stand a slim chance of getting the summons withdrawn, but if their case is sound, which I guess it is otherwise why would the OP agree to pay to dispose of the allegation, that would really be a goodwill gesture by the TOC now.
I agree that the TOC will win the case and the OP will end up with a conviction if it goes to court. That much at least is a 'racing certainty'.
That is why the OP should take steps to try and get the summons withdrawn and stay out of court, because there he will lose.
He might like to look at likely costs + fines if he goes to court based on similar prosecutions in his area. He should aim to settle at any level up to the total for similar cases in his area, and maybe above and beyond that if he is serious about avoiding the conviction. Perhaps he could call the magistrate's court and ask the clerk what this is likely to cost him in court, I'm sure they handle many such cases.
If someone doesn't pay for 3 weeks it is reasonable to assume that they do not intend to, so the OP needs to explain clearly that he was waiting for his pay cheque and apologise for not sending any kind of letter in the mean time to explain the delay.