But it was while preparing to defend the Branson court challenge that mistakes in managing the West Coast bidding process were found.
Mr McLoughlin scrapped the bidding and suspended bidding on other franchises. In addition, three DfT civil servants were suspended.
Mr McLoughlin also announced that two independent inquiries would be carried out - the first to look specifically at the West Coast bidding process and the other to investigate franchise bidding generally.
FirstGroup had been due to take over the London to Scotland West Coast route on December 9. Virgin has been asked to carry on for the time being, with a two-year interim franchise to be offered later followed by a longer, permanent franchise.