SPOILERS AHEAD YOU HAVE BEEN WARNED
As you find out after finish the last chamber, you have two paths you can choose. You can either place a few portals and leave the facility, or you can go back into stasis. Below are my interpretations of what each ending means, feel free to leave comments if you know more specifics than I do.
The Stasis Ending
In this ending, you follow instructions and you go back into stasis, with the expectation that you will be woken up in time to stop the singular threat to the Aperture Science facility that occurs between the present and future timelines. This singular threat could be one of several things, including Chell’s destruction of GLaDOS in Portal 1, but the most likely of these is when Wheatley takes over the facility in the Portal 2 timeline and causes major destruction, so you would be trying to stop Chell one way or another.
The fact that you are never woken up from stasis in Portal: Reloaded likely indicates that your stasis chamber failed, like so many others, as described in Portal 2. It is also possible that something happened to the AI responsible for waking you up, which is supported by the fact that the AI seems to be failing in the escape ending. Given that the chambers were playable throughout Portal: Reloaded, it is doubtful that your failure to wake up was from physical damage to this part of the facility. It is also strongly implied that you are dead or in permanent stasis.
Despite the fact that you should have been able to stop the threat, something failed and you were not given the chance to change the future. While somewhat sad, I think this works nicely for fitting the game into the Portal and Portal 2 timelines without raising questions.
The Escape Ending
In this ending, you divert the funnel, travel to the future, and make it out of Aperture Science. The triple portal device stops working once you are out of the facility, and several standard zombies (humans taken over by standard headcrabs) are on their way to get you.
For those who don’t know Half Life, Headcrabs are omnivorous, parasitic alien organisms that latch onto and control human hosts using their claws, mouth, and beak. While the human host can sometimes be saved if the headcrab is removed quickly enough, such a takeover usually results in death of consciousness. The resulting creature is hostile towards other humans.
Obviously you never get to stop the incident as you were supposed to, but it doesn’t really matter because it doesn’t get stopped in either ending. Similar to the Half Life franchise, you have the potential to get away from the zombies or kill them, but since you find yourself in a forest setting with a defective portal device and likely no other weapon, I’m not sure how well you’ll fare. Furthermore, based on Portal 2’s ending, it is unlikely you can re-enter Aperture Science after getting outside. A full-blown headcrab zombie apocalypse is not likely what is implied; it’s far more likely that this is an abandoned patch of civilization at least several miles from any humans that haven’t been infected by headcrabs. While I would say the protagonist likely dies, it’s anyone’s guess; feel free to use your imagination.
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