Holmes and Watson spend most of Game of Shadows exploring their relationship much as they explored it in the first movie, by pursuing clues, battling villains, and admiring each other's manly assets.
"Lie down with me, Watson!" As he issues this command, Sherlock Holmes (Robert Downey Jr.) is prostrate on the floor of a train cabin, wearing a disheveled dress, his mouth smeared with red lipstick. These remnants of his disguise as a lady passenger -- such that Dr. Watson (Jude Law) would not spot him -- grant the scene all sorts of entendres. As Watson complies and the camera hovers over the men beside one another, Holmes looks pleased, lighting his pre-post-coital pipe as Watson asks, so coyly, "What are we doing down here?"
This may be the perennial question for Holmes and Watson, perhaps particularly as they are imagined for the Guy Ritchie franchise. At this moment in Sherlock Holmes: A Game of Shadows, Holmes is grappling with his partner's marriage, just completed. None too pleased, that Watson and the wife, Mary (Kelly Reilly), have been riding the train to their honeymoon spot in Brighton, Holmes has tagged along (in his gaudy disguise), because he knows what Watson does not, that Professor Moriarty (Jared Harris) means to murder the couple. If it's not likely that Holmes would much miss Mary, he is, as ever, determined to preserve Watson. After all, he explains -- after this moment on the cabin floor erupts into especial mayhem, that is, a barrage of bullets ripping through the walls, missing the men on the floor -- "Your nuptials were rather poorly timed; our relationship, er, our partnership, has not fully run its course!"
With this, Holmes invites Watson on a sort of substitute honeymoon, to Paris, where it happens that Moriarty is lecturing. Here Holmes also pursues the mysterious and very athletic fortuneteller, Madame Simza (Noomi Rapace), whose beloved brother Rene (Laurentiu Possa) is mixed up with the anarchists who have been bombing key sites in Europe. While her gypsy crew undresses their guests (each article of clothing a prize in its own way), she and Holmes plot to recover the brother, reportedly immersed in an assassination plot and disguised by way of experimental surgery. (The profound possibilities of this movie-magicky disguise make clear, if you need the reminder, the jokiness of Holmes' rudimentary efforts; here his goofiest, which he calls "urban camouflage," make him invisible in drawing rooms.)
Rene and the assassination plot are means to Moriarty's end (a war between Germany and France) as well as a way for Holmes and Watson to reinforce their commitments to one another. It may or may not matter that a second brother, Holmes' own, Mycraft (Stephen Fry), shows up to annoy Watson (his primary purpose seems to be calling Holmes "Sherly"). As the film deploys multiple plot strands, none of them seems especially central, save for the relationship, er, partnership, that will grant the franchise forward motion.
To that end, the boys spend the rest of Game of Shadows exploring that relationship much as they explored it in the first movie, by pursuing clues, battling villains, and admiring each other's manly assets. The backdrop this time has to do with terrorism (of course it does), or so it seems. In fact, the anarchist bombings that propel Holmes and Watson's investigation are cover for another, more insidious plot about war profiteering. With a munitions factory already online (producing automatic and also very large guns), Moriarty pauses to explain the obvious: “War on an industrial scale is inevitable. All I have to do is wait.”
As it turns out (more or less historically), Moriarty will have to wait some time for World War I, but his prescience, in the film's version of 1891, emphasizes his super-villainy and also his status as a match for Holmes' superior intellect. Here again, this is made manifest when Holmes shows he can pre-envision fights, mostly so Ritchie can show off his bullet-timeish expansion of these fights. This means you see each contest at least twice; when Moriarty reveals his own capacity for pre-envisioning, this number increases.
Visually clever as they may be, these Rube Goldbergian progressions are less about plot than characterization. Both Holmes and Moriarty believe themselves to be the smartest guys in any room, and as they imagine what they might make happen, they reveal their incapacity for imagining that someone else might imagine something else. In the first film, these pre-visions enhanced your perception of Holmes' brilliance, his ability to see into an immediate future because he anticipates so accurately. This time, the pre-envisioning is complicated when two individuals engage in it, and only one of them is able to see what the other might.
As plots within plots, the pre-visions are good enough metaphors for the film, which posits Holmes and Watson's ostensibly evolving relationship as a plot within another (or more precisely, within several). Though it remains the principal focus of the franchise, it is (as in most buddy cop movies) disguised as subplot (and so perhaps resembles the outfit Holmes puts on to look like a chair).
Again the partners are mutually admiring, and again they maintain their hetero distance, sometimes distracted by weapons and other times dallying with women: there's Mary, of course, and also a bit of Irene Adler (Rachel McAdams), who briefly appears in order to be turned into Holmes' motivation to chase down Moriarty. This chase is framed as well as by Holmes' insistence that he means to save Watson (and oh yes, Mary) from the supervillain. But really, it's his way to bring Watson back into the "partnership," because they can only get their man if they work -- or lie down -- together.