The world has ended, again. Durandal's early awakening of Thoth was not enough to prevent the Pfhor from firing the trih xeem, and the W'rkncacnter has laid waste to the universe again.
The second of the alternate endings also takes place on a segment of Aye Mak Sicur, in fact the same one as Aie Mak Sicur. In fact, it seems to be exactly the same level: Same geometry, same monsters, same item placement. However, this time the station is in a vacuum (rendering the rockets and M-75 ammo useless). Perhaps it took some damage during the battle, and sprung a leak. You'll still face Hunters and Juggernauts, with the occasional S'pht'kr reinforcements, and you'll still run into dead ends where the station has been cut off.
The terminal, this time, seems to be written by one of the S'pht ancients, possibly S'bhuth. It is in green text, with no document details, and in the disjointed speech of the S'pht's English translators. He says that everything is over and lost, and that there is no future here. The last line I think means that whoever is writing this has been made completely free by the destruction, he no longer has any purpose (resistance is futile, so why bother trying... foreshadowing the final screen?) or any responsibilities (anything he had obligations toward is destroyed), so he is finally in control of his destiny. But at what cost...
The Marine doesn't want to pay that kind of price for his own freedom. There must be a better way. In every universe so far, the Pfhor use the trih xeem when Durandal defeats them. Trying to help Durandal prevent the Pfhor from using it has always failed. But what if the Pfhor were to win... It might be worth the loss to prevent the W'rk's release. And the only one who could possibly defeat Durandal is Tycho. The Marine is about to try playing for the other team again.