Clues in Part 1 that point specifically to Maggie:
- At one point, Burns remarks that stealing Springfield Elementary's oil was "like taking candy from a baby", and expresses a desire to actually steal candy from a baby. Admittedly, this clue is only obvious in hindsight.
- When Burns collapses onto the sundial, his hands point to the letters "W" and "S". From Burns' perspective, however, the "W" looks like an "M": "MS" is Maggie's initials. Throughout the episode, every clock is set to either 3pm or 9pm - DVD commentary indicates that this was to teach the viewer to interpret the sundial upside-down.
- During the town hall meeting, Burns asks the townspeople, "Who here has the guts to stop me?" The townspeople are seen glaring at Mr. Burns before reluctantly looking away... all except Maggie, who continues to glare.
Clues in Part 1 that eliminate other suspects before they are exonerated in Part 2:
- Anyone whose initials don't contain an S and a W/M is eliminated right off the bat.
- When Homer enters Mr. Burns' office to spray-paint his name, his head briefly blocks a sign saying "ONLY IN" so that it reads "NO", with a small arrow pointing to him.
- If you watch really closely as Burns falls onto the sundial, you can see his gun is missing, hinting he was shot with his own gun. This instantly eliminates everyone who was seen carrying a gun at the town meeting: Smithers, Moe, Skinner, and Barney. It also eliminates Grampa Simpson, who was seen earlier in the episode with a Smith & Wesson. Even if you miss this clue, you can still eliminate:
- Moe, because he's carrying a shotgun, and Burns was shot with a pistol;
- Skinner, because his gun had a suppressor (and why would he take it off?);
- Smithers, who leaves in the opposite direction to Burns. He mentions during the town meeting that he never misses Pardon My Zinger, and an ad in Moe's Tavern reveals that show is on at 3pm, the time at which Burns was shot.
This still leaves a few other suspects, however: the ones that spring to mind are Groundskeeper Willie and Tito Puente, who are both only exonerated in Part 2. Furthermore, the clues pointing to Maggie are very subtle, with no hard evidence. So while it's possible to suspect Maggie, if you pay close enough attention to Part 1, I don't believe it's possible to conclusively prove it was her until the reveal at the end of Part 2.