The first one has you doing all sorts of awesome random stuff that's still cool while trying to track down this super rogue agent (Thorian, Rachni? Damn cool.)... only to find out he was being controlled with by his sentient spaceship... they drop the bomb that the super advance race didn't just up and disappear, but that there's a whole slew of these thinking evil spaceships and they wiped out all life in the galaxy. Then you watch the controlled agent blow his brains out only to be reanimated in the final confrontation as you prevent the ship from starting the annihilation of the entire galaxy.
The second one says kills Shepard and magically renanimates him in a "we developed the technology to do this, but can only do it the one time and only for you" lame excuse to allow new players to create a custom looking character and have the abilities start at zero again. Then you get told "oh, we need you, colonies are being attacked and disappearing". You find out it's these ripoffs of the aliens in independence day, have a confrontation or two, go to the second reapers base and witness that they're building a giant t-1000. You kill it and leave.