In my first few play throughs of ME2, I saved the base for Cerberus but after beating talking to Sovereign on Virmire , I saw it was a bad idea. Sovereign himself tells you why the reapers left the mass effect relays behind after each genocide; to have future organics use the technology the Reapers want them to. And according to the prothean VI, The Reapers also had control of the keepers through indoctrination, but thanks to the protheans, that control was taken away. The VI also said that since organics were unpredictable that it was logical that soverign would use The geth as pawns instead of indoctrinating any other organics. Which raises the question why did The Reapers indoctrinate some of the protheans and create the Collectors? why not just use synthetics to gather and harvest humans? Maybe because Harbinger had direct control with all collectors so control wouldn't be able to be taken away. But I think their main purpose is just like the mass relays, to have organics follow The Repears desired technology pipeline.
I like it, I always thought the game could use more double-edged swords. If you leave the ship the IM gets cocky with his new tech and tries to bum rush the reapers only to then have the reapers cut said technology.
I haven't been able to decide on this. Although I did blow it up in all my playthroughs up-til now, I am wondering if l should keep it for the save that I will be using for ME3. Here's my thoughts:
Why KEEP IT:
1. For the reaper tech that may be found in the human-reaper larva which will help fight the Reapers.
2. To get knowledge about protheans that may help to activate the weapon that punched a hole in a Reaper with one shot (see DERELICT REAPER) and made a canyon on Klendagon.
Why BLOW IT: Most of this depends on The Illusive Man's actions:
1. Timmy may go berserk with the tech obtained from there and and destroy or enslave every other alien race for humanity (and for himself) and cause total galactic war. Meaning Reapers or no Reapers, few races may go extinct.
2. Timmy has all the resources to make a Human-Reaper. A human-reaper larva that is sentient but has no legs (Timmy can easily give him some legs without killing any humans). EDI which has some of Sovereign's cybernetic software. And the Thanix Cannon of Normandy which is the miniaturized turian version of Sovereign's cannon. Re-activating the Human-Reaper may spell doom for all sentient life in the galaxy as it may go rogue (assuming TIM can control it in the first place) and activate the Citadel relay to zap the Reapers from dark space to the heart of the galactic community in half a second.
you know what: never trust guy with that eyes
I mean how many villians are there with odd eyes? how many goodies?
plus glow of blue star you get for blowing ship suits IM more than red so just tell him you're his creative designer
Honestly I think what you did with the Collector base won't matter much. If the advanced technology were going to be decisive in stopping the Reapers, Bioware wouldn't have given you the option to destroy it....and if using it somehow dooms the galaxy to either Reaper genocide or Cerberus tyranny, you wouldn't have been allowed to keep it.
There's also the fact that the Collectors themselves were using this stuff and they couldn't stop you....so taking it and reverse-engineering it probably won't make a big difference in the end.
Base will have about as much effect as the decision on saving/ abandoning the council in ME1. A few lines and references.
I fully expect that due to the massive attack on Earth Shepard will be joining the alliance once again and all the references will be like:
Andersen: "Shepard! You shouldn't have left Cerberus with that base intact! There've been lot's of Cerb related reports about attacks on our alien allies recently - ones with advanced cybernetic implants. But it's not time to dwell on it. Go get the Reapers!"
Shepard (paragon): "It seamed to be the right choice, Sir! I'm off the kick the reapers until they are extinct!"
Shepard (renegade): "How dare you questioning me !? If not for me, you'd be pudgy slime! I can't take this anymore.. I'm off to take the fight to the reapers."
Shepard (indecisive): "Sir! Yes Sir!"
Andersen: "I'm glad you destroyed that base you've talked about, but looking back that tech would have come handy."
Shepard (paragon): "It was for the good of galactic civilization! We'll forge our own way."
Shepard (renegade): "All our enemies must perish! Now for the reapers!"
Shepard (indecisive): "Sir! I think it had to be done, Sir!"
Oh and you'll hear maybe 1-2 "galaxy news" report about Cerberus on rampage or the Omega relay acting strange lately. No further effect (no missions).. maybe an e-mail from Miranda/ EDI/ TIM with some explanation, rambling.
seeing how this'll be the end of the trilogy, i suppose the effects gonna be a little more than an e-mail or news report.