Gerard managed to make his way to London by pretending that he was looking for a lost falcon, to allay suspicions as to why he was off the road. Apart from being briefly detained by a suspicious village watch, he made it safely to London to meet with Father Henry Garnet, the Jesuit Superior.

Gerard quickly developed a strong following amongst the Catholic gentry. Being educated in all the habits of a gentleman such as hunting and gambling, as well as his fashionable dress, enabled him to pass undetected as a priest in their society, and quietly win souls to the church. Mary Digby was later to exclaim her astonishment at discovering his true identity as priest, "Why the man lives like a courtier." He would play adeptly at cards, but with Ave Marias at stake instead of money. But his sincere devotion and pleasant modest manner was such that he alone of the Jesuit priests remained completely untarnished by the Gunpowder Plot.

Even Dr. Jessopp, a Protestant says of him:

The extent of Gerard's influence was nothing less than marvellous. Country gentlemen meet him in the street and forthwith invite him to their houses; highborn ladies put themselves under his direction almost as unreservedly in temporal as in spiritual things. Scholars and courtiers run serious risks to hold interviews with him, the number of his converts of all ranks is legion; the very gaolers and turnkeys obey him; and in a state of society when treachery and venality were pervading all classes, he finds servants and agents who are ready to live and die for him. A man of gentle blood and gentle breeding - of commanding stature, greate vigour of constitution, a master of three or four languages, with a rare gift of speech and an innate grace and courtliness of manner - he was fitted to shine in any society and to lead it. From boyhood he had been a keen sportsman, at home in the saddle, and a great proficient in all country sport. His powers of endurance of fatigue and pain were almost superhuman; he could remain in hiding days and nights in a hole in which he could not stand upright, and never sleep, and hardly change his position: he could joke on the gyves that were ulcerating his legs. He seems never to have forgotten a face or a name or an incident. Writing his autobiography twenty years after the circumstances he records, there is scarcely an event or a name which recent research has not proved to be absolutely correct. As a literary effort merely, the Life is marvellous. ("Academy", 9 July, 1881, The Catholic Encyclopedia)

But extreme danger was always present. Gerard had a narrow escape in October of 1591, while attending a meeting of Jesuit priests at Baddesley Clinton, owned by Anne Vaux and Eleanor Brooksby. It was raided by pursuivants at five o'clock in the morning, Anne Vaux and the alert servants buying time to enable the priests to hide. He evaded capture by standing in ankle-deep water in a sewer converted to a hiding-place for over four hours along with Father Henry Garnet, Father Robert Southwell, Father Edward Oldcorne and six others.

Gerard moved to Braddocks, the home of William Wiseman, his wife Jane, his mother also named Jane, where unbeknownst to the household, a trusted servant had become a spy. The mother, Jane Wiseman's house was the first to be searched, and the old woman was arrested and put on trial in London. But she refused to plead guilty or not guilty. If she had been found guilty, her estate would have reverted to the crown. By refusing to plea, she was guilty of "Peine Forte et Dure", for which the sentence was to be pressed to death, however she could still transfer her estate to her children. On 30 June 1598 she was sentenced to be stripped naked and have stones and iron put on her, and being given only bread and water, but not to eat on the day she drank, and not to drink on the day she eats. Jane Wiseman was more than prepared to meet this death, but the Queen's Councillors, worried about the outcry in London if this was carried out, commuted this sentence, and she remained in prison until the accession of James I.

Gerard's house in London was the next to be raided; luckily he had decided at the last minute to spend the night with Father Garnet, but his host, William Wiseman, was arrested along with several others.

Then Braddocks was raided on Easter Monday, 1 April 1594, and Gerard had to quickly conceal himself in a hiding place under the grating of a fireplace. In the rush, all he had with him was a couple of biscuits and some quince jelly. The pursuivants locked up the household and began tearing the place apart. After two days of no luck, they decided to take the household members to London for examination, leaving behind a few servants and the pursuivants to continue the search.

His hostess was now in great fear that Gerard would die of starvation if she was taken away. She was glad to see that one of her trusted servants was staying behind, and gave him instructions on how to call Gerard out of his hiding place when no one was around. She was not aware that this servant was in fact the traitor, and he immediately gave this information to the authorities. The search resumed with renewed vigour, and guards were posted in every room. One night, some of the guards decided to light a fire in the grate above Gerard's head, and because the false bottom was made only of wood, he had to avoid the burning embers that fell upon his head. The guards knocked away a brick, and noticing the wood underneath, commented on it, and that they should investigate it the next day. For some reason they forgot.

After four days, they thought that Gerard had to have escaped, and released Jane Wiseman, and left her to her destroyed house. She barred the doors, and called Gerard out of his hiding place, wasted and weak with hunger, and cramped from spending four days in such a confined space. He discovered that his mistress during the entire four days had refused to eat herself, so that she would know his condition and if he could still be alive.

But his luck quickly ran out and he was finally captured a few days later on April 23, at a new lodging he had taken in London, along with Father Garnet's servant Nicholas Owen, the expert craftsman of many of their hiding-places.

During his questioning before the commissioners, headed by Sir Thomas Egerton, he made it clear that he would not answer any questions that involved others. He was open about being a Jesuit priest, and when accused of being 'sent to seduce people from the Queen's allegiance to the Pope's, and to meddle in State business.", he responded that this was no concern of his, and that the Jesuits were under strict prohibition to have anything to do with matters of State.

Not satisfied with his answers, they had him imprisoned in the Counter in the Poultry. At an examination with a magistrate called Young, and the notorious Topcliffe, "old and hoary and a veteran in evil", who was a "cruel creature and thirsted for the blood of catholics", Gerard upset Topcliffe by refusing to sign a confession of Topcliffe's devising, writing his own statement in a disguised hand, with his signature written extremely close to the text, denying Topcliffe the opportunity of getting a sample of his handwriting or adding anything to the statement. Furiously, Topcliffe told him that "I will see that you are brought to me and placed in my power. I will hang you up in the air and have no pity on you." He then had Gerard clapped in irons.

Friend bribed Young to have Gerard moved to the Clink after three months of being in chains, a change which Gerard describes as being the difference between "Purgatory and Paradise", and where he had more freedom to carry out his priestly duties. He even managed to convert the son of his gaoler, who succeeded to the job on his father's death. He left this position to join a catholic household, but was captured and held prisoner in the very place where he was the gaoler. But after the capture of some boys he had arranged to be sent abroad, and the death of Young, who made quite a sum in bribes from catholics for their protection, he was moved to the Salt Tower in the Tower of London, and his examinations resumed by William Waad and Topcliffe.

But he held firm in his cautious statements. When admitting that he would indeed reconcile a hundred thousand to the Church, he also said that these "would be the Queen's men. They would not be against her. We hold that obedience is due to those in authority". But he would not name names or assist them in locating Garnet, so a warrant was made out for his torture.

They took me to a big upright pillar, one of the posts which held the roof of this huge underground chamber. Driven in to the top of it were iron staples for supporting heavy weights. Then they put my wrists into iron gauntlets and ordered me to climb two or three wicker steps. My arms were then lifted up and an iron bar passed through the rings of one gauntlet, then through the staple and the rings of the second gauntlet. This done, they fastened the bar with a pin to prevent it slipping, and then, removing the wicker steps one by one from under my feet, they left me hanging by my hands and arms fastened above my head.

When asked if he would like to now confess, he refused.

But I could hardly answer the words, such a gripping pain came over me. It was worse in my chest and belly, my hands and arms. All the blood in my body seemed to rush up into my arms and hands and I thought that blood was oozing out from the ends of my fingers and the pores of my skin. But it was only a sensation caused by my flesh swelling above the irons holding them.

But Gerard, in spite of moments of temptation, had his simple faith on his side. "God in His infinite goodness and mercy have me the grace of resignation, and, with a desire to die and a hope (I admit) that I would, I offered Him myself to do with me as He wished. From that moment the conflict in my soul ceased, and even the physical pain seemed more bearable than before.." He was hung like this for several hours, only relieving the pressure on his arms when he fainted.

Gerard was tortured on three separate occasions, without revealing anything, and they decided to move forward with a trial. Gerard almost seemed disappointed that he was not given as hard a battle as other priests who had died for the cause, saying that he was "clearly unworthy of their prize". He was unable to move his fingers for three weeks.

In front of the Queen's Attorney General, Gerard responded to the question of how he could be anxious for the conversion of England, and still keep out of politics:

If I could fulfill all that I wish and desire, I would want the whole of England to return to Rome and the catholic faith: the Queen, her Council, and yourselves also, and all the magistrates of the realm; yet so, my Lords, that neither the Queen, nor you, nor any officer of state forfeit the honour or right he now enjoys; so that not a single hair of your head perish; but simply that you may be happy both in this present life and in the life to come.

He also defended the doctrine of equivocation, of which through his writings we can see he is undoubtedly an expert - "Against this I maintained that equivocation different from lying. In equivocation the intention was not to deceive, which was the essence of a lie, but simply to withhold the truth in cases where the questioned party is not bound to reveal it. To deny a man what he has no right to is not deception.", and proceeded to provide examples of Jesus' use of the doctrine.

Pending his trial, John Gerard contrived his escape with fellow prisoner John Arden. With the assistance of friends from the outside and of the warder, on the night of 4 October 1597, they fastened a rope from a tower across the moat, and the rope being almost horizontal, they had to inch their way along the rope to safety. Gerard, still being weak from torture, barely made it across, but was soon safe in the hands of his friends and fled the vicinity by boat. Taking a horse provided for him, he fled to Robert Catesby's house Morecrofts, in Uxbridge, to meet up with Garnet, where he spent a few days to get his strength back.

Gerard then moved into the household of Elizabeth Vaux, whose husband George Vaux had recently died, leaving her with six children and inconsolable grief. He resumed his life of pastoral work, hiding and close calls.

He converted many to the Catholic cause, including the conspirator Sir Everard Digby. "To me," say Gerard, "he was always a most loyal friend, and we might have been brothers in blood. In fact we called each other 'brother' when we wrote or spoke to one another". In spite of his accomplishments under extreme circumstances, he remained modest. "What I did" he said, "is nothing compared with what others did."

Gerard became suspicious of his friend Digby's activities and reasons for moving his household, as he later outlined in a letter to Digby when he was imprisoned in the Tower after the discovery of the Plot:

Finding all things hidden out of the way and many of your household gone...I asked you what was become of them. And when you told me you had sent them into Warwickshire, and your hounds also, and yourself were going presently after, about a hunting match which you had made, though I seemed satisfied for the present because a stranger was there with you, yet...I did soon after (when I had compared many particulars together which seemed strange unto me) draw you into a chamber apart, and there urge you to tell me what was the reason both of that sudden alteration in your house and of divers other things which I had observed before, but did not until then reflect upon them so much, as, for example, the number of horses that you had not long before in your stable, the sums of money which I had been told you had made of your stocks and grounds, which (said I) in one of your judgement and provident care of your estate, are not likely to be done without some great cause, and seemed to think you had something in hand for the catholic cause." (PRO SP 14/18)

Gerard was obviously correct in his suspicions, but his friend denied that anything was going on, because he knew full well that Gerard would try to deter him from it. Digby, his other vacillations notwithstanding, never wavered from his claim that Gerard knew nothing of the plot.

Once the Plot was discovered, a proclamation was issued against Gerard, Garnet and Tesimond, and Gerard was forced once again into hiding during a nine day search of the house at Harrowden. During that time, he wrote an open letter protesting his innocence and contrived to have copies scattered about the streets of London and refuting the charges allegedly made against them by Robert Catesby's servant and co-conspirator, Thomas Bates. He escaped from Harrowden, and bravely made his way to London, where he stayed for some time before realising that he was such a wanted man that he had no choice but to flee the country.

He was assisted financially by Elizabeth Vaux, and on May 3rd, the day of Garnet's execution, he crossed over to the continent dressed in livery in the entourage of the Ambassadors of Flanders and Spain, after a short bout of cold feet on their part.

Gerard lived the rest of his life relatively quietly. Early in 1607 he was appointed British Penitentiary at St. Peter's, and two years later sent to Flanders to help found the English Province at Louvain, where he wrote his "Autobiography" and perhaps also his "Narrative". In 1614, he became the first Rector of a Jesuit school of theology at Liege, and in 1622 became the Rector of the house of the English Jesuits at Ghent. In 1627 he became confessor at the English College at Rome, where he died ten years later at the age of seventy-three.

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