Sir Thomas Clifton’s life illustrates well the trials and tribulations that beset Catholics in England in the 17th century. It could be said that while Anglicans preached passive obedience and non-resistance (until put to the test by James II), Catholics practised that policy in the face of much greater provocation.
Late in life he was prosecuted for high treason, and the evidence given at his trial illuminates the contrast between the preference for peaceful co-existence of the cradle Catholics in the country and the proselytising enthusiasm of the convert Catholics and Jesuits who surrounded James II. This contrast has recently been fully explored by Steve Pincus, as well as much earlier by both Macaulay and John Lingard.
Lingard notes that when the king was considering the repeal of the test act many Catholics,
… aware that the spirit of discontent was stirring, deprecated any alteration which might afterwards provoke a reaction. They deemed it imprudent to risk the tranquillity which they enjoyed for the pursuit of a greater but uncertain benefit, and were content to submit to the privations imposed by the laws, provided they might be relieved from the penal and sanguinary statutes prohibiting the private exercise of their worship. 
Pincus goes further and suggests that some of the country Catholics may have been active opponents of James’s reconversion ambitions and not necessarily ‘… cautious men, temperamentally unwilling to risk unsettling their provincial tranquility, …’ 
Sir Thomas, who was one of these country Catholics, was born in 1628, one of 14 children. He married twice, having several children by his first wife, Bridget, who all died young except one daughter, Mary, who married the sixth Lord Petre. By his second wife, also Bridget, he had two children, Thomas, born in 1668 and who died in 1688, and Bridget. Sir Thomas died on 13 November 1694. 
Four, possibly five of his sisters became nuns in the Spanish Netherlands, usually with the Poor Clares at Gravelines.  Putting daughters in foreign convents at this period, while usually requiring a hefty dowry that only the gentry could afford, was often preferable to marrying them off, which could call for a more costly dowry. 
In the 17th century the Cliftons lived at Lytham and practised as Roman Catholics, suffering various penalties and trials for their faith. They were Royalists in the Civil War which cost the lives of Sir Thomas’s elder brother, Cuthbert, and three of his uncles and resulted in the sequestration of the family estates. Sir Thomas had four younger brothers: John, William, Richard and James. One of his sisters, Bridget, married Thomas Westby of Mowbreck. He was made a baronet in 1661 ‘as a recognition of his family’s loyalty.’ In 1678-9, at the time of the Popish Plot, Sir Thomas and his wife Bridget were indicted for recusancy. 
When James II dismissed the Earl of Derby as lord lieutenant of the county in 1687 along with his deputy lieutenants and replaced him with the Catholic Viscount Molyneux, Sir Thomas was appointed as one of the new deputy lieutenants. This would have angered the many Protestant Tories among his neighbours. 
Sir Thomas was arrested at least twice in company with other Catholic gentleman at the time of the revolution and shortly afterwards. The dates and occasions of his arrests are somewhat confused. Bellingham in his diary entry for 17 December 1688, which details local events following on from William of Orange’s arrival in England, records that ‘Sr Tho Clifton was taken and brother’.  This is the only record found of this event.
According to Thomas Patten, in his evidence at the Manchester Jacobite trials (see below), Sir Thomas was arrested on 16 June 1689 and held at Patten’s Preston house. This is supported by a document in the Kenyon papers dated October 1694 which supplies information not contained in Patten’s evidence, that on 16 June 1689 ‘… another party of Collonel Mathews’ dragoons went to Lithom, Sir Thomas Clifton’s house … and there took up Sir Thomas Clifton and brought him prisoner to Preston.’ The document reveals that Sir Thomas was one of several other prominent Catholics held at Preston. The others were transferred to Manchester on 25 June and held until the following January, while Sir Thomas remained detained in Preston. 
Lawrence Rawstorne, one of the signatories to the transfer order, seems to have given little credence to the notion of a local Catholic conspiracy, while recognizing the fears that gave rise to such ideas. In a letter to Roger Kenyon dated 18 December 1689 he writes, 
This world, this degenerate age wee live in, is soe addicted to lyeing, that one can credit nothing beyond their owne knowledge. The storie of hideing armes at Sir Thomas Clifton’s, when fixidly examined, amounts to nothing; the persons that should have proved it, denies flatly, they never saw armes, nor did any expressions ever come from them that they did. Mr. Rigby, of Riby, tould me uppon Monday last, that hee was urgent with theim to tell the trueth therein, but they know nothing of any such matter; this account I had from him on Monday last, and so could not write sooner. The countrey is troubled with the fears they lye under of the Irish Papists who are, under bail, at liberty, and it is thought many more appear under that pretext, which did not before. House-breakings and stealing of horses, and such rumors of misdemeanours are abroad, as are strange to hear; and yet not an information come[s] to mee about any. What such things will result in, I cannot define, but deme them presages of some ill consequences and effects; the Lord turne all to the best!
Sir Thomas was again arrested in July 1694, being held first at Chester and then at Tower of London before being brought to Manchester in October where he was tried for high treason for his part in the ‘Lancashire Plot’.
Thomas Patten of Preston appeared in support of Sir Thomas:
Thomas Patten Esq. produced as a witness on behalf of Sir Tho. Clifton. Declared that he being one of the Deputy Lieutenants of Lancashire in the year 1689, received orders from the Lord Lieutenant to secure severall Popish Gentlemen, that amongst them Sir Tho. Clifton was one who was taken and brought Prisoner to Preston, upon the 16th day of June 1689. That Sir Tho. being a very infirm man, and unfitt to be carried so far as Manchester, which was the place where the rest of the Popish Gentlemen then made prisoners were secured, Mr Patten undertook for Sir Tho., and prevailed to have him kept at Mr Patten’s own house in Preston, where he continued prisoner, and was not discharged till January following at which time all the Gentlemen were set at liberty. That during Sir Tho. Clifton’s confinement he expressed to the said Thomas Patten much zeal and affection to the present Government, saying how much the persons of his religion ought to be satisfied with their usage, as putting no difference betwixt them and other Subjects, save in the public exercise of their Religion, so long as they themselves would be quiet; that he often protested for himself that he could never endure to think of practising any change, and Mr Patten further said that he knew Sir Thomas’s disposition to have always been peaceable and quiet.
Sir Thomas and his fellow defendants were acquitted on 22 October. Sir Thomas was dead within a month. 
 John Lingard, A History of England, 3rd ed., vol. 14 (London: Baldwin and Cradock, 1831), 82–3.
 Steve Pincus, 1688: The First Modern Revolution (Yale University, 2009), 139–42.
 ‘A Genealogical and Heraldic History of the Commoners of Great Britain and Ireland Vol 2 – John Burke – Google Books’, 57, accessed 2 March 2016, https://books.google.co.uk/books?id=jJFIAQAAMAAJ&dq.
 ‘Who Were the Nuns?’, accessed 10 March 2016, http://wwtn.history.qmul.ac.uk/counties/lancs.php?place=Clifton%20|%20Westby%20%26%20Clifton%20|%20Westby,%20Clifton%20%26%20Lytham.
 B. G. Blackwood, ‘The Catholic and Protestant Gentry during the Civil War Period’, Transactions of the Historic Society of Lancashire and Cheshire 126 (1976): 5.
 ‘Townships: Clifton-with-Salwick | British History Online’, accessed 2 March 2016, http://www.british-history.ac.uk/vch/lancs/vol7/pp161-165; William Dugdale and F. R. Raines, ‘The Visitation of the County Palatine of Lancaster: Made in the Year 1664-5’, The Chetham Society, OS, 84 (1872): 86–87.
 D. P. Carter, ‘The Lancashire Militia, 1660-1688’, Transactions of the Historic Society of Lancashire and Cheshire 132 (1983): 181, http://www.hslc.org.uk/documents/PDFS/1982.pdf.
 Thomas Bellingham and Anthony Hewitson, Diary of Thomas Bellingham, an Officer under William III (Preston: Toulmin & Sons, 1908), http://archive.org/details/diaryofthomasbel00belluoft.
 ‘DDKE/HMC/888 “The Following Account of Lunt Is What Hath Been Attested by Particular Witnesses, Not Otherwise Worth the Reading, but as an Index, If Turned To, to Show from the Circumstances of Times and Places, What Construction May Be Made as to the Truth or Improbability of His Evidence, with Some Deviations Observable to the Same Purpose.”’, Lancashire Archives Catalogue, October 1694, http://archivecat.lancashire.gov.uk/CalmView/Record.aspx?src=CalmView.Catalog&id=DDKE%2fHMC%2f888&pos=3.
 ‘DDKE/HMC/423 Letter from: L. Rawstorne to Roger Kenyon – Newhall.–I Am a Little Troubled to Hear of the Confidence of Our Red-Lettered Gentlemen. Shall We Not Live to See Their Combs Cut, or Their Tethers Made Shorter? Portion of Seal.’, Lancashire Archives Catalogue, 26 November 1681, http://archivecat.lancashire.gov.uk/CalmView/Record.aspx?src=CalmView.Catalog&id=DDKE%2fHMC%2f423&pos=1.
 William Beamont, ‘The Jacobite Trials at Manchester in 1694. From an Unpublished Manuscript’, Chetham Society, 1st, 28 (1853): 98–9.