Harlequin found Excalibur during the events of Harlequin's Back, but the nature of the plane in which the runner's receive the sword is also worth mentioning.
In the adventure, the runner's traverse a few isles and encounter characters from the Arthurian mythos, including Lancelot, Nimue and Galahad. In part of it, they detect that the island may contain the once and future king.
Right before Pendragon showed up in England, the isle of Lyonesse shows up smack dab in the middle of the Channel, reportedly the return of the Arthurian isle.
It is also possible that the sword, while found by the runners, never leaves the island.
There is also the theory that the Pendragon is the actual Pendragon, Rhonabwy, the Welsh red dragon that adorns the nation's flag and that Arthur and Merlin saw fighting a white dragon.
It should be noted that The Laughing Man himself comments on the idea that the Pendragon's sword is Excalibur(Shadows of Europe) by posting "Excalibur, indeed? Interesting..." Whether this denotes that Excalibur no longer resides with Harlequin or if this is yet another example of the jester's snide contempt is up for interpretation.
In 6WA, some propose the idea that the Pendragon is an actual dragon, but Frosty shouts that down by saying that if it were, the other dragons would have taken an interest in it's shenanigans and that she is not convinced. This implies that it might not be Harlequin, because others would be interested in his shenanigans as well and that Frosty, Harlequin's journeyman, is ignorant of Pendragon's identity. Or that could be a misdirect on Harlequin's bequest.
As for the Harlequin is Arthur, Dunklezhan is Merlin theory, Harlequin does have a rather famous conversation with "Ambrose" in Virtual Realities 2.0 that suggests Ambrose is Ambrose Merlin, Arthur's tutor.
So, my conclusion is that it is either Harlequin, Rhonabwy or actual Arthur returned from the metaplanes. All would have an interest in taking down he LPO and the NDM.
I prefer the last theory, as 6WA suggests Queen Caroline has a soft spot for the Pendragon and the idea of the royal lines merging pleases me.