Nice work.
I only have some complaints:
1. Voice acting sounded nothing like the original characters.
2. When there were the Agent Smiths, the word you are looking for is "assimilate," not "annihalate." Assimilate is to make an induvidual part of a whole(which is what the rogue program Smith does). Annihalate is to utterly destroy(like what the Death Star does to planets or monkeys banging on pots and pans does to a person's hearing).
Good parts:
1. Everything that was supposed to be funny was funny. The "cookie monologue" was the best, though. "WHAT IF I FAIL TO EAT THE COOKIE???!!!!"