This is mostly for my own reference because I get conflicting stuff from wiki and the canonwiki. And since I've watched every episode like five times, why the hell not. Oh, and spoilers for both seasons and to be edited when new stuff comes up.
Six years ago
- Six and White team up. ("Six Minus Six")
Pre-Nanite Event (dated possibly a few months before the explosion)
- Several rich corporate CEOs greenlight the Nanite Project ("Dark Passage")
- They all settled in Geneva/Europe in order to start work. ("Mixed Signals")
- The scientists (we know so far) involved: Cesar Salazar, Rafael and Violetta Salazar (Rex's parents), Gabriel Rylander, Van Kleiss. ("Mixed Signals")
- There was dissent in the group. Half wanted full completion of the project, to do proper testing. The other half wanted to launch it straight away. (The people listed above are most likely for the former. Yes, even Van Kleiss) ("Mixed Signals" "Dark Passage")
- They got into a fight and Rex (age 10) was injured. Badly. They used one of the test nanites in order to save him. His abilities are a "side-effect". ("Mixed Signals" "Dark Passage")
- Seeing Rex's abilities pushed the latter faction to trigger a replicating cycle with the nanites. ("Mixed Signals")
- Program ZAG-RS is created for trapping stray nanites from leaving their tanks. Given Violetta's voice. ("Written in Sand")
The Nanite Event (Five Years Ago)
- EXPLOSION!!! (Rafael and Violetta perish, Rylander escapes to South America, Cesar is stuck in sublight drive and Rex loses his memory. No fucking clue what happened to Van Kleiss)
- Replicating cycle is triggered! Which means there is an infinite supply of nanites in the air. It doesn't matter if you're born before or after the event. If you're alive, you have nanites. The end.
- A chunk of Europe is a dead zone or an overrun monster-zone. EVEN THE SOIL. (from the looks of the map, I'd say parts of France, Switzerland and Germany) ("The Day Everything Changed" "What Lies Beneath")
- Kiev, Ukraine is overrun with monsters. The world's governments place a Containment 1 field over it. Is now known as the "Bug Jar". ("The Forgotten")
- Engineers are shunned and hated. ("The Architect")
- One goes EVO. ("Divide By Six")
4 - 3 years ago
- Rex resurfaces as Quarry's lieutenant in Hong Kong. Does bad things, has his own gang. Already knows about his own memory losses and seems deeply paranoid about it. ("Rabble")
- He gives his gang to Quarry in exchange for his own freedom. ("Rabble")
- Rex loses his memory.
- The governments get together to form the organisation known as Providence.
3 - 2 years ago
- Providence is still building its foothold. ("Promises, Promises")
- Rex appears in Mexico City. He is discovered by Six and taken to Providence. ("Promises, Promises")
- Head Researcher Dr. Fell is replaced by Dr. Holiday. ("Promises, Promises")
- The Petting Zoo is built. ("Promises, Promises")
- Purgatory and Paradise Base are established for Rex's surplus nanites.
- The term E.V.O is pegged and promoted. ("Promises, Promises")
- White Knight becomes Head of Providence. ("Promises, Promises")
- Van Kleiss becomes known to Providence.
- "Incurable" and "Curable" E.V.Os are categorized.
- ZAG-RS forms a community for engineers. It has evolved into a sentient computer that wants the destruction of all nanites. ("The Architect")
- Greenville, Ohio goes missing. Literally. ("Breach")
- The law says you can defend yourself against EVOs ("The Hunter")
Current year
- Providence and E.V.O are now household terms. Everyone knows who they are.
- Paradise base is wiped out ("Frostbite")
- The Great Wall of China is destroyed ("The Swarm")
- Van Kleiss surfaces as a terrorist. ("The Day Everything Changed")
- Cesar returns ("Mixed Signals")
- Providence controls the jails (yes, even the human ones as Hunter Cain had to bribe a Providence Guard to escape) ("Night Falls")
- People all the world come to Rex for a cure. There are mobile units set in various locations to make Rex accessible to the public. ("Exposed")
- Gabriel Rylander is killed. ("Dark Passage")
- Rex gains the Omega-1 Nanite, a control nanites that allows him to use blueprints to create builds. Given to him by Gabriel Rylander. ("Dark Passage" "Payback" "Mixed Signals")
- Van Kleiss can create E.V.Os ("Payback")
- ZAG-RS is captured and rebooted ("Written in the Sands")
- Dr. Brandon Moses builds a machine that can isolate the nanite bonds and supercharge. Holiday figures out how to separate them. However, this procedure still needs to be perfected as it's not mentioned the episode after. ("A Family Holiday")
Six Months Later
- White is replaced by Black Knight. ("Lions and Lambs")
- They use brainwashing to control EVOs. ("Back in Black")
- Cesar stays with Providence.
- White Knight, Six, Holiday, Bobo leave Providence and form a new base.
- Ben 10 appears along with "Alpha" ("Heroes United")
- The Bug Jar is destroyed (no sign of NoFace) ("Heroes United")
- Parallel worlds theory is established.
- The Sphinx is destroyed along with several pyramids.