Ah. This debate again.
Let's summarise the regular arguments:
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- Why can't the Reapers switch the beam off?
- Maybe it takes a while to switch the beam off? Maybe they never anticipated having to switch it off in a hurry?
- Okay... Why not just blow it up?
- Well, it does act like a miniature relay - that might blow up the Earth for all we know. Remember Arrival?
- Now you're just speculating.
- It's a video game! We all are!
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- Why doesn't Harby shoot Normandy?
- Stealth systems & Reaper IFF.
- Uh... The Normandy is right there. It's perfectly visible. Stealth systems wouldn't work since that's infrared light, and it's visibly not a Reaper.
- EDI's electronic countermeasures & jamming from the beam.
- Harbinger seems to be doing a perfectly good job shooting troops and vehicles, so the jamming from the beam doesn't seem to be bothering him. And do you really think EDI could jam a Reaper? Let alone the biggest, baddest Reaper in the fleet?
- Harbinger's got more important things to worry about. He needs to focus on the troops, not a ship that's actively evacuating troops.
- Yes... but blowing up the Normandy would trigger a fairly large explosion. Probably wiping out most of Hammer squad.
- The Normandy does have Silaris Armour and upgraded barriers. Harbinger would need a few shots. And in that time, some of Hammer might get through the beam.
- Really? You're arguing that Normandy could take a direct hit from Harbinger? The codex says that no ship has survived a direct hit from a Reaper main gun.
- They're in atmosphere. That would reduce his shot power.
- Nowhere in the codex does it say that atmospheric drag affects mass effect weaponry.
- Yes, but real world physics says that they can't be firing at relativistic speeds. Look at this. If they are, every shot ought to be a nuke.
- Oh, come on. We have no idea how mass effect weaponry would work in the real world. Don't use XKCD on me.
- Fine. In the opening, we see a cruiser (referred to as a dreadnought by Ash/Kaidan) taking multiple direct shots from a Reaper. If Reaper can ordinarily one-shot us, that implies the atmosphere does reduce weapon strength (somehow).
- You can sit and watch that cruiser get hit by as many Reaper shots as you like. Doesn't count.
- At minimum, running through that section, it still takes two shots.
- Ugh. Forget I asked...
- Actually, hang on. You said Harbinger needs to focus on Hammer squad or else some of them might get through. But we see him pause, not shooting anything, during the cutscene. Why doesn't he shoot the Normandy then?
- Maybe his guns are recharging? We see him take similar pauses during the charge just beforehand.
- We don't hear any blasts during the cutscene either.
- Eh. Artistic license. The focus of the scene is on the goodbye. Loud explosions etc would distract from the drama. Shepard is presumably just tuning them out.
- That's the best you've got?
- Yup.
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- Why is only Harbinger present? What happened to the other Reapers we saw heading towards London? Heck, why not call in all those hundreds of Reapers in orbit?
- They're needed in orbit to defend against Sword and Shield Fleets.
- This is the Reapers we're talking about. I'm not sure that Sword and Shield has them under that much pressure.
- I wouldn't be so sure. We did spend an entire game assembling the biggest, most badass fleet ever.
- I'm sure they could spare a couple more ships. In fact, we saw them sparing a couple more ships.
- Maybe those Reapers were needed elsewhere in London?
- What could possibly be more important than defending the beam?!
- Crushing the London FOB to prevent a second push? The Reapers are arrogant, they figured Harbinger would be enough for the beam.
- If so, they were idiots.
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- Why not just nuke London from orbit? It's the only way to be sure...
- See my earlier argument that blowing up the beam might blow up the Earth.
- I didn't like that argument the first time.
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- Okay, why doesn't Harbinger just shoot Shepard? Sure, maybe shooting Normandy would take more than one blast to get through the atmosphere/ shields/ armour/ whatever. But Shepard is just standing there. Wouldn't take more than a second.
- Still focusing on Hammer? We did throw a lot of troops at that beam. Besides, Harbinger does shoot Shepard.
- And epically fails to kill him, leaving it up to Marauder Shields and the three Husketeers.
- Well, on Insanity, Marauder Shields kills me more often than he doesn't...
- NOT THE POINT!
- Fine. Yes, Harbinger should have melted Shepard's body into the ground, but he doesn't. Clearly he's never read the Evil Overlord List.
- (Disappears for a couple of hours because that link leads to TV Tropes.)
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At the end of the day, it's a fictional universe where nothing will ever be fully explained. It's impossible to prove that there's no possible explanation.
I'm personally willing to assume that there are in-universe explanations for why stuff happens, we just never see the explanations ourselves. However, I can understand why that scene might break a person's Willing Suspension of Disbelief. Perhaps Bioware should have thought the scene through a bit more, but nothing's ever going to be perfect.