S.H.I.E.L.D. makes it's first appearance within the MC2 in A-Next #4 via an appearance from Agent 33 (not to be confused with the Main Marvel Universe's Agent 33 also created by Tom Defalco and Ron Frenz) who is tasked with protecting the Wakandan ambassador, N'Kano and the Wakandan prince, T'Chaka during their visit to America. Notice Agent 33 wears a yellow and blue-black S.H.I.E.L.D. uniform.
Shortly after within the pages of Spider-Girl #5 we first learn of the organisation's Maximum Security Facility at Mount Athena, New York. It's here we glimpse the Venom Symbiote, who's been imprisoned here for over a decade. Notably, the unnamed S.H.I.E.L.D. Agent's seen here wear yellow (or perhaps orange?) and black uniforms.
The very next week, in A-Next #5, we get another appearance from members of S.H.I.E.L.D. operating in Latveria's former capital Doomstadt. Here we see a few more Agents, this time clad in more standard looking military attire, attacked by Doombots while searching for a missing girl. We learn that thanks to political bickering, even S.H.I.E.L.D. is forbidden to set foot within Castle Doom. After the Avengers recover the missing child, they provide S.H.I.E.L.D. with a false story to hide the existence of Kristoff Vernard. This is also our first reference to Nick Fury in the MC2.
The title goes for 3 in a row with another S.H.I.E.L.D. appearance in A-Next #6 when the Avengers team accompanies Argo to the Mount Athena Facility in search of his father Hercules. Agent 33 returns to give intel to the Avengers team, advising them no one on-site has clearance high enough to know the identity of 'The Merchandise' (in actuality an insane and grief-stricken Hercules himself) but 'the Top Man himself' approved the Avengers team to take over custody.
Over in Fantastic Five (Vol. 1) #2 we witness the titular team field-testing the invention of Dr. Lenny Gilcrest, 'The Superoid,' for S.H.I.E.L.D. Things go awry when Gilcrest is knocked out by the villainous Dominator disguised as a S.H.I.E.L.D. Agent. Dominator and the rest of the Wizard's Warriors take control of the Superoid and attempt to steal it, coming into conflict with the F5 and S.H.I.E.L.D. Interestingly, Dominator mentions she used to work for S.H.I.E.L.D. Note the Agents of S.H.I.E.L.D. are garbed in yellow and blue uniforms.
We don't see S.H.I.E.L.D. again for quite some time until Spider-Girl #86 when we revisit Agent 33 at the Mount Athena Facility as Apox the Omega Skrull escapes his containment deep beneath the mountain. Notice again that the various S.H.I.E.L.D. Agents all wear the seemingly standard yellow and blue-black uniform.
After this, S.H.I.E.L.D. is mentioned to be attempting a rescue of Nova and Earth Sentry following the destruction of their spacecraft by Galactus' herald Dominas (Last Planet Standing #3).
We see some familiar faces among S.H.I.E.L.D. Agents during the Carnage story arc in Amazing Spider-Girl #9-12 with Maria Hill (more on her in the future!) and Contessa Valentina Allegra de Fontaine and the shadowy Director of S.H.I.E.L.D. himself, Nick Fury all making their MC2 debut. We also see a more tradition S.H.I.E.L.D. colour scheme for the first time here with white on black uniforms.
Next up we have Fantastic Five (vol.2) #4 in which a freshly returned and cosmically-empowered Doctor Doom forcibly ejects S.H.I.E.L.D. forces from Latveria. Here, the S.H.I.E.L.D. forces are seen in the military attire seen previously in A-Next #5. Later in the issue we get our first and only glimpse of a Helicarrier in the MC2 as we learn of it's destruction.
For the final appearances of S.H.I.E.L.D. in the MC2, we turn to the American Dream mini series. These appearances are tricky. Maria Hill shows up so you'd think she was working for S.H.I.E.L.D. but dialogue and recap pages both state she's working for the National Security Force. I'd be inclined to accept that Hill simply changed employers since her last appearance, except every issue after she shows up in American Dream #2 clearly depicts her in full S.H.I.E.L.D. uniform leading other agents also clad in S.H.I.E.L.D. uniform. Perhaps I could cover this further at a later date, but for now, I'll simply include these appearances.
That's it for present-day appearances, but we also see S.H.I.E.L.D. Agent Sharon Carter in flashbacks in both Spider-Girl #32 and American Dream #3 in addition to mentions elsewhere. For a bit more on this see The Carter Family Tree.
That's it for S.H.I.E.L.D. in the MC2. I find it interesting that all of the organisation's appearances prior to the Amazing Spider-Girl series seem to feature a distinct variation of the S.H.I.E.L.D. uniform with the yellow and blue-black colour scheme, while all appearances since feature the classic white and blue-black uniform colours. It brings to mind this old Official Handbook of the Marvel Universe entry:
Until I master spy craft and become a secret agent tasked with obtaining unpublished MC2 stories from Tom and Ron's desks, I remain
frogoat