BS Angel has made various references to companion cubes, so, my theories:
A: We will be breaking/entering into an aperture science facility, either on the ship or otherwise, and somewhere there will be a pile of companion cubes (WITH THE HEART) and possibly having to solve a couple of tests to escape.
B: If we go far off the beaten path, we will make a couple of jumps, and find a portal gun. We will see a portal-surface behind us, and across a canyon. We will portal across, and find a lone companion cube.
C: BS Angel has no friends, so needs her companion cube for company.
Edit: Don’t ask me how I got two polls. Vote in the SECOND POLL, as the results show before end of poll.
Why thank you. Sucks to think that these BS threads above/below are covering this entirely justified and evidence-incited conversation. A lot of the speculation has far less evidence than a comment from BS Angel herself. “…under the companion cube like box…”