User blog comment:Suparockr/List of Plotholes throughout the series/@comment-6810992-20130301002900/@comment-1440333-20130301005045

On horizon - kaiden / ashley get paralyzed by seekers, but left there? As does about half the colony, due to Shepard and crew showing up and robbing the Collectors of the element of surprise and driving them off.

'why is the collector ship / collectors - hive/bug creatures? they were protheans, supposedly the most technically advanced things in any known cycle. they didnt fly, and wernt bugs. is it just the way they have been re-written by the reapers? or just that when they made me3 they decided to make protheans different to the hive collective?' Probably a bit of both. Think of the Collectors as Prothean husks.

'me1 - protheans are long, tentacle creatures... look nothing like they do now?' Actually those statues are only shown on Ilos, revealed by Javik to be an insunannon planet. Presumably those statues are insunannon.

'Why is Anderson on the citadel? how did he get there? through the same beam of light? but he wasn't behind you right?' He came through behind of you, but ends up scattered by the beam, similar to the drift of a ship coming through a relay (explained in the codex) and so ends up ahead of you.

'ok... now we are on the citadel.. why... is it totally destroyed inside? why are the carcasses that resemble the collector ship here? why are the keepers all hunky-dory? why doesnt anyone just grab a keeper, shake it and go "TALK TO MEEEE".' The keepers are not really sentient, and they break if you interfere with them (codex). Also the Reapers are harvesting, and so are presumably constructing a Reaper from human tissue on the Citadel, perhaps how they did it in previous cycles as well - The Citadel always falls first remember.

'oh hell illusive man!! - oh wait, you are indoctrinated... and whenever he talks to you about something negative you get these "headache style" pains and the screen shudders?. dont worry, im not interested n how or why you got here!' we already found out the IM was on the Citadel from Vendetta. He has implanted himself with Reaper teach which has presumably given him biotic type abilities, similar to Saren's implants. And obviously Shepard is grievously wounded.

oh wait is this the same kid i saw at the beginning of the game...nevermind Yes, because the kid is representing Shepard's guilt. Presumably the Catalyst, an advanced AI, interfaced with Shepard and chose a suitable form.