Link and Zee's relationship is another example of love in the films. One of the messages of the trilogy is that love is power. Neo and Trinity perform some of their most amazing feats because of love (for example Neo flying at impossible speeds to save Trinity and her taking on a room full of armed henchmen to save Neo).
I have imagined this moment for so long...Is this real?
At the end of Reloaded Morpheus had nothing left to live for - it was brutally revealed to him that everything he believed in was a lie, all his visions of freedom and truth suddenly shown to be just another system of control. When the Nebuchadnezzar is destroyed he says "I have dreamed a dream, and now that thing is gone from me". This is a direct quote from the Bible, the passage is referenced on the back of the white car during the freeway chase; DA203 (Book of Daniel chapter 2 verse 3). I don't have space to go into details of the symbolism here, but in terms of the storyline the dream he mentioned is the prophecy, obviously.

You may have noticed that because of this Morpheus plays a much lesser role in Revolutions. Most of his screen time is spent obeying Niobe's orders aboard the Hammer. At the very end of the film Morpheus gets a new meaning to his life - Niobe.
Neo... wherever you are... thank you...
The "barge" machine which carries Neo away looks much kinder than the machines we've seen before. Throughout the sequels it is implied that the machines are equal to if not better than humans. Where they're taking his body is a mystery, but with Neo now being the Source I assume they would preserve his body somewhere safe.

Also, during this scene you can hear a very faint heartbeat, further confirming that Neo isn't dead.
The object at the centre of this image is Neo, as bright as the DEM was (the previous real world manifestation of the Source). The shape made by the machine's tentacles and head resembles a lotus flower... where the law of karma works no more. The Buddhist law of karma no longer applies when one reaches Nirvana, as Neo is said to have done. This is also referenced in the lyrics of Neodammerung.
The black cat was seen in the first film, when "they change something".
The Matrix is reloaded with Neo's new knowledge of choice, perfecting it. This is shown by the Matrix losing its green tint, as you can see in the higher quality shot below.
Well now, isn't this a surprise?
This can be seen in the Zion Archives (at thematrix.com), although it wasn't in the film. Like the barge scene, it shows that the machines actually care for Neo now. Perhaps they always had this nature, or perhaps it was imparted to them by Neo's reload (after all, Neo experienced love at a more personal level than the other Ones)

This is also the first time we see green plant life in the Matrix.
Architect: You played a very dangerous game


Oracle: Change always is...


Architect: Just how long do you think this peace is going to last?


Oracle: As long as it can...What about the others?


A: What others?


O: The Ones that want out.


A: Obviously they will be freed.


O: I have your word?


A: What do you think I am, human?
If you listen carefully at the end of the first Matrix film, you can hear a certain type of music being played as Neo ascends to a new level of being. At this point in Revolutions you can hear this music again...
Oracle, Oracle!

Sati is an important character - she is the first program to exist without a purpose. She can alter the Matrix program as she sees fit, now accepted as "legal" in the Matrix because of Neo's reload (Neo knew that sentient life didn't need a purpose, but the machines didn't as shown by Smith's speech).
Sati: We were afraid we might not find you

Oracle: Everything's okay now.
Look, look!
Just look at that! Beautiful!









Did you do that?
For Neo.
That's nice. I know he'd love it.
Sati:Will we ever see him again?



Oracle: I suspect so...
...some day.
Did you always know?
Oh no, no I didn't. But I believed. I believed.
Belief is a strong theme in Revolutions. Belief, like love, gives us power. Remember how a boy only 16 years old was able to save the last free city just because of his belief in Neo ("Neo... I believe").
The last shot is of Neo in all his glory, at the end of his Christian, Buddhist and Hindu journey.
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