MPs will arrive back in Westminster next week under a new and threatening front after the storm cloud that cast such a long shadow over Parliament before they left for the summer holidays.

At 9am on Monday letters will go out in the internal mail to all 645 MPs detailing the results of Sir Thomas Legg’s audit of their past five years of expense claims.

Any hope that politics can return to normal before the imminent general election campaign may turn out to be forlorn, with dozens of parliamentarians facing difficult and damaging questions that could have an impact on party leaderships as much as individual MPs.

Most of the letters are understood to clear Members of significant wrongdoing, while those transgressors who have already repaid sums totalling more than £500,000 to the taxpayer will have at least some protection against further shame being heaped on their heads.

Others, however, who escaped censure in the summer’s disclosures will face being dragged into a second wave of a scandal that threatens to dominate politics for the rest of this year.

Sources close to the process say that Sir Thomas has been particularly exercised by three specific areas of alleged abuse.

The first of these is evidence that MPs have used allowances to repay the full cost of mortgages on their second homes, rather than merely the interest, as rules allow.

A number of MPs, including the former Cabinet minister Clare Short, have already been forced to repay thousands of pounds for breaching this rule.

But many have complex mortgage arrangements, which have been opaque to both the Commons Fees Office and Sir Thomas’s inquiry. Although he accepts that some errors may have been inadvertent, he is expected to ask dozens of MPs to provide full details of their loan agreements so that any overpayments can be identified.

The Times has been told that Sir Thomas is also concerned about claims for two other areas: gardening and cleaning.

MPs are allowed to claim for basic garden maintenance, such as lawn-mowing and hedge trimming, but not for “plants, shrubs, flowers, hanging baskets or other decorations”. Instead, some are said to have used the allowances for the purposes of “beautification — even landscaping” — of their gardens.

A similar picture has emerged over cleaning costs. Sir Thomas is said to have found evidence that, far from employing someone only to vacuum carpets twice a week, a few MPs have used their expense allowances to pay for people who are “virtually housekeepers”.

Most controversially, the letters going out next week are believed to reinterpret some of the rules retrospectively, with MPs being asked to repay expenses that may have breached the spirit, if not the letter, of the law.

One parliamentary official said: “It is very hard to make judgments about these things without making judgments about MPs who have explored the ambiguity of the existing rules. Legg has interpreted his terms of reference in such a way as to give him quite a lot of latitude in moral persuasion.”

MPs facing further questions or demands for money on Monday will have three weeks to prepare their case before being referred to the Members’ Estimate Committee, chaired by John Bercow, the Speaker.

Some of those who have already seen their careers wrecked by disclosures in The Daily Telegraph this year are looking to Sir Thomas for vindication. Julie Kirkbride, the Tory MP for Bromsgrove who was forced to announce that she was quitting politics, is among those hoping that the Legg report will salvage her political future. “I do believe I am innocent of the charges levelled against me. I hope the Legg inquiry will demonstrate this,” she said recently.

Any such cases will reflect badly on party leaders including Gordon Brown and David Cameron who have been criticised for taking draconian or panic measures against their MPs at the height of the furore.

In a sign that the committee is braced for ferocious lobbying, resistance and even legal action from MPs desperate to save their seats, if not their reputations, the committee is not expected to release its report until December.

This will include, however, not only details of the audit but also a full list of expenses claims made in 2008-09 — without the acres of black ink blanking out details, a practice that exposed publication of earlier years’ expenses to widespread ridicule this summer.

By the time that the new report is published, Sir Christopher Kelly is expected to have produced his proposals for cleaning up the discredited system. Early hints about what the Parliamentary Commissioner for Standards will do suggest that he will recommend a ban on MPs employing family members. There are also rumours that he has considered whether to stop Members taking out mortgages on second homes with the assistance of the taxpayer.

Either measure would be greeted with fury from MPs, many of whom are already asking themselves whether it is worth remaining in politics.

“We have already been through the mincer once. Legg is doing it to us again — and then we have Kelly,” a senior MP said yesterday. “This is not just a double whammy, it is a triple whammy. The next few months are going to be very grim, I fear.”