Agent Torres mentions that Agent Quinn is taking care of her mother. In real life, actress Jennifer Esposito left the series to take care of her mother.
This is the first season premiere to have absolutely no reference to Anthony "Tony" DiNozzo. However, Bishop introduces us to "floor time", very much like Tony's "campfires", they are brainstorming sessions. So while he isn't mentioned there is still a hint of him.
IMEI stands for International Mobile Equipment Identity, it is a number used to identify a phone across multiple national & international mobile networks. While a phone's Subscriber Identity Number (SIM) can change, when the SIM card is changed, the IMEI is a number unique to the phone, it does not change even with a different SIM card. This makes it easier to track and/or block a person's phone even when it has a different SIM card; if someone's phone's IME number is blacklisted (say for criminal activity or if the phone is stolen) they cannot make calls on the phone's network, and often other networks as well, even if the SIM card is changed.
McGee seems to have gained weight while being held prisoner.