No One Lives Forever/WMG

Isako never wanted to really kill Cate.
Her code of honor didn't allow her to rebel to the Director, but she saw a very worthy opponent in Cate, the one that could really bring H.A.R.M. down. So, she didn't strike a fatal blow to her in Japan, knowing that her UNITY colleagues were nearby and would have certainly saved her from bleeding to death. It is also possible that Isako, after jumping out of the tornado in Ohio, rescued an unconscious Cate - after all, we don't see what happened between the end of that battle and Cate awakening in the hospital bed. And she might have known of the death trap machine's sabotage (see below), if she didn't sabotage it herself.

The big-nosed mook sabotaged the machine that should have killed Cate.
He is among the ones brought to safety by Cate and Armstrong after escaping from the collapsing underwater base. Later, just before the death trap is activated, he calls the Director because of another call from his mother but does it very awkwardly. We don't see him anymore afterwards. Maybe he wanted to distract the Director? His might have been a gesture of gratitude towards Cate.

General Hawkins is in league with the Director.
In a cutscene, we see Hawkins in a bar, brooding about how they don't allow for his all-out war plans, casually meeting a man who is very happy to converse with him - the Director. This isn't brought up again, but later we can see that both men are quite happy about the idea of starting World War III... Maybe this point was meant to be brought up in future episodes, if they will ever be made.

No One Lives Forever and Timesplitters share a universe.
It struck me that Timesplitters has a lot of colourful villans. Colourful villans that enjoy building elaborate deathtraps and leaving their lackeys to finish off spies when it's highly likely the spy will kill all the lackeys and escape. They both have uniformed mooks, also. While most of this can be attributed to gameplay, it can be imagined that many of the villans Harry Tipper faces could belong to H.AR.M., with a chance that Harry himself could be working in conjunction with UNITY.

H.A.R.M stands for....
Hateful And Really Mean