We last saw Captain Halley on July 11, 1699 when he moored his ship Paramore at Deptford and brought his first voyage as master and commander to a close: but what has he been getting up to since then?
He kept no diary and so we must look for him in other documents, such as correspondence and minutes, and though these don’t offer any glimpses of his domestic life, it’s surely not too fanciful to picture him entertaining his wife Mary and daughters, Margaret and Catharine, with seafaring tales, and getting to know his three-month-old son.
We do see him at several meetings of his erstwhile employer, the Royal Society; he didn’t make the meeting held the day after he arrived at Deptford but he was there a week later on July 19 when he entertained the Fellows by showing a “Branch of a Barbados fig tree, which having many nerves or long fibres, which falling downwards, hang so yt they touch ye Ground, where they take root, and so grow up again”. 
He followed this up at the next meeting by presenting “part of a viviparous plant as he called it, which grows by the salt water side, called [?]Guapaiaira ye Mangrave; Dr Sloane said it is mentioned and figured in ye Hortus Malabaricus.” 
He seems not to have attended the August 2 meeting but on August 9 he was back again with another specimen, this time showing the seed of his “viviparous plant” (a mangrove brought back from Brazil) and Hans Sloane again informed the Fellows that it was “very well described and figured in ye hortus Malabaricus.” 
On the 16 August, Halley enlivened the final meeting before the summer recess by showing “Several Variations of the Needle he had observed in his Voyage, set out in a Sea chart, as also he shewed yt Brazile was ill placed in ye common Maps, and he shewed some Barnacles, which he observed to be of quick growth.” 
Robert Hooke’s diary had ended by this date and so we have no recorded sightings of Halley in London coffeehouses, but it’s a safe bet that he spent time there, hearing the news and catching up with his friends – and perhaps passing round his botanical exotica.
He was apparently spoken of in wider London society as Narcissus Luttrell mentions his voyage and the court martial of his Lieutenant, though Luttrell’s account is largely erroneous, wrongly reporting the crew were minded to turn pirate and that Harrison was declared “uncapable for ever of serving his majestie by sea or land”, when Harrison was actually found not guilty. 
But Halley is most visible in the Admiralty records, where we learn he attended the Lords of the Admiralty on July 21 to ask that he “may be a second time sent out, for the perfecting his designe of discovering the variation of the Compass” and that their Lordships were “inclinable to allow [it]”, given the “good that may thereby accrue to ye Publique”. 
There was evidently some (unjust?) criticism of Halley by their Lordships after Harrison was found not guilty at the court martial, and so you might think that Halley would have been happy just to secure a second commission – but he went on to complain about the sailing qualities of the Paramore and ask for another ship!
The Admiralty ordered Deptford to survey the Paramore and report on her condition, and the dockyard advised that they could make alterations to settle her more in the water and help find her trim and then “here is noe Vessell … more fitting then she is for that Service”. 
So whatever Halley’s wishes, he’s not to be parted from his Paramore just yet.
UPDATE AUG 2017: BOTANICAL SPECIMENS FROM HALLEY’S VOYAGE
Sometime after I published this post in August 2013, I came across a reference in one of James Petiver’s catalogues to plants that had been given to him by Halley and the ship’s surgeon, George Alfrey – and it occurred to me that if these specimens had gone into Petiver’s collection, and that collection later went into the Sloane collection, which in turn formed the founding collection of the British Museum, then these specimens might yet be extant.
Sloane’s natural history collections are now held at the Natural History Museum, and on the advice of Dr Anna Marie Roos (@annamarieroos3), I contacted Dr Charlie Jarvis, who very kindly spent an hour in July 2015 showing me the relevant specimens in one of the Petiver-Sloane albums. Most of the specimens have only a botanical name attached, but one or two also have a date and location and so can be assigned to either the first or the second voyage. The specimen I’m showing here was collected by Dr Alfrey in Brazil in March 169 on the first voyage, and is described as a “Mangle [mangrove] Brasile”. There is rather more to be said about collecting activities on the voyages, and I may write about that elsewhere in future – but for now I offer this specimen of a Brazilian mangrove (with apologies for the poor photo!).
 Royal Society, JBO/10, pp 139-140
 Ibid, p 141. The Hortus Malabaricus is well worth a look: here’s a short introduction to the work, with a selection of illustrations
 Ibid, p 143
 Ibid, p 145
 Narcissus Luttrell, A Brief Historical Relation of State Affairs, Vol IV, pp 532 & 538
 National Archives, ADM 2/397, pp 153-4
 National Archives, ADM 106/3292, f.100v