- Despite the sheer horror of the geth's backstory, the fact that they are still searching for quarian survivors/descendants, preserving their homeworlds, and protecting their artifacts to the point that they actively pursue looters shows that they truly cared about their Creators.
- The geth ask Ambassador Chambers if humanity will help them recreate the quarian species. Chambers immediately says yes.
- Granted, the "heartwarming" aspect is somewhat undermined when it turns out that at least part of their reasoning for resurrecting the Quarian Race is a way of saying "Fuck You" to the Ethereals, meaning that humanity is recreating a galactic power from nothing more than genetic scraps and tissue fragments out of spite, but still heartwarming that they're so determined to do it.
- The scene on Athena where the XCOM team comes to secure Alma looks like its going to head straight into pure Nightmare Fuel, and Alma herself is presented as terrifyingly dangerous and unstable. XCOM has no idea how they're going to get the girl to go with them, right up until she sees James Vega, an uplifted grizzly bear, and instantly stops crying, and runs over to him with a child-like giggle and fascination. Then he gives her a ride out on his shoulder.
- A strange case, but the fact that Harlan Wade is actually a Papa Wolf, as opposed to his horrific canon iteration.
- It turns out that Alma and James stay together as a team all through her XCOM training as a psionic. Shepard even refers to James as Alma's "sanity bear."
Heartwarming / Vigil