In this episode (which continues the plot from the season opening episode "One"), Adam confronts two antagonist agents at a gym, and one of them draws his weapon which is an IMI .50 Desert Eagle. This is an unlikely weapon of any covert agent (it's large, heavy, bulky and noisy and has a low ammunition capacity) and probably a reference to the system agents of The Matrix (1999). In this double-episode of "Spooks" a faction within the political and business realm of Great Britain tries to instate unchecked "security measures" not dissimilar to those upheld by The Matrix's agents.
The poetry given by Malcolm to Harry at the end of the episode [to be read at Colin's funeral], 'Comrades mine and I in their midst, and their memory ever to keep for the dead I loved so well' is by Walt Whitman, from When Lilacs Last In The Dooryard Bloom'd. Whitman's sexuality is often discussed alongside his poetry. Though biographers continue to debate his sexuality, he is usually labeled as either homosexual or bisexual. Malcolm, after Colin's death in the previous episode, is distraught at the loss of his friend - the choice of poem intimates a closer relationship than friendship between Malcolm and Colin.