Stream:
Now that they succeeded in making the dimensional area, they have one more task for this project; trying to make it appear somewhere else besides Sci-Lab! Of course, this is no easy task, since the only way they can get it to be somewhere else is to use unmanned crafts that contain dimensional area generators, and that can only go a short distance. To make matters worse, giant viruses are attacking all over the world! Netto and Enzan have to fight without a dimensional area in the first episode of Stream, since they were arriving, so they counter attack a giant Metaur virus by comically hitting in the head with steel beams being controlled by Rockman and Blues (LOL!). When they defeat it using Cross Fusion, Rockman doesn't return, because he was captured by Forte (Forte is a powerful Net Navi who made his first appearance in EXE Area 2, but I forgot to mention him. sorry! ^.^;) Forte wants Rockman's and Blue's Ultimate Programs, so he can become powerful enough to take on an extraterrestrial Navi name Duo, who wants to erase the Earth from exsistense because he sees it as too dangerous. Although, he gives the Earth one more chance to save and prove itself that its a safe planet, by giving 13 people a sign on their hands known as the "Crests of Duo" and sending Navis known as Asteroids to test the humans by seeing if their selfish, greedy, cruel, etc.Since these crests enhance the Synchro rate, all 13 of the crest-holders know how to Cross Fuse.
This season focuses mainly on Cross Fusion, so don't be surprised or annoyed if you see all of them Cross Fusing at once.
Guess who's back? Dr. Regal! Although supposedly was to be destroyed in Axess, he's back, and this time he has a knew army of Darkloids; Swallowman, Cosmoman, Blizzardman, and Cloudman! Also, Shademan, a Net Navi from Axess, bit Rockman on the neck (sort of like a vampire), causing him to become evil! However, his dark side eventually splits from his good side, resulting in Dark Rockman. But, later in the series, Slur, Duo's assistant and right-hand lady, deletes him, and he rejoins with his good side.
In the end, the Cross Fusion members are ultimately defeated by Duo, and he splits the humans from their Net Navis. The Navis defend their Net Ops, saying that they would do anything for them. Duo doesn't understand why they are still defending them, and decides that he will delete the Navis, as well. However, Netto and the others won't let that happen, and Barrel, one of the Cross Fusion members who came to the future 20 years ago, realizes that Duo is interested in Cross Fusion. So, Barrel lets Duo use a technique similar to Cross Fusion that is from Duo's planet, in exchange for sparing the Earth. Peace is restored, well, at least for now, anyways.

Episode:1
Forte wants Rockman's Ultimate Program to gain power to defeat Duo. (Talk about power-hungry, huh? -.-)

Episodes : 3-51
The Progress PET is different from the Advanced PET in many ways. It has a 3-D touch screen where you can slot-in battle chips, or you can use it the traditional way. Like the Advanced PET before it, it comes in different colors depending on your Navi (i.e. Rockman-blue, Blues-red, Searchman-green)

Episodes: 3-10, 16, 18-22, 24, 25, 27, 28, 30, 31, 33-35, 37-41, 43, 45-48, 50, 51
With a knew PET comes a new appearance in Cross Fusion! Episode 3 was the first time they showed Netto's Cross Fusion sequence, while episode 4 was the first time he did his Cross Fusion pose (shown above).

Episodes: 3-5, 7, 8, 15, 29, 31, 32, 45, 48, 50, 51
Enzan's Cross Fusion is in the same episode as Netto's, since they were both fighting Asteroid Beastman. Once again, episode 3 was the first time they showed Enzan's Cross Fusion sequence, while episode 4 was the first time he did his Cross Fusion pose (shown above).

Episodes: 17, 18, 26, 41, 42, 48, 50, 51
At first, like I said before, Laika hated Cross Fusion due to using raw power instead of smarts. But, seeing that Asteroids have the ability to make it to the real world
without dimensional areas using chips called "Dimensional Chips," Laika decides to join Netto and Enzan in the fight against Duo.

Episode: 17
Since Laika was given the ability to Cross Fuse, all three of the main Net Saviors know how to Cross Fuse. So, I thought I should put this in! :-D

Episodes: 21, 25, 31, 47, 50, 51
Yuriko worked for Dr. Regal throughout all of Axess. Now, Dr. Wily, her foster father, has given her a Synchro Chip so she can Cross Fuse to help save the world with the others.

Episodes: 28, 38, 40, 46, 48, 50, 51
In Axess, Meiru had a dream that she would someday Cross Fuse so she can fight together with Netto. But, in this season, its a reality! Using Rush, a cybernetic dog who can go into both the human world and net, she can Cross Fuse using a certain type of Synchro Chip called the "Rush Synchro Chip." ^.^

Episode: 36
After Rockman temporarily became evil (unlike Blues' case T.T), due to Shademan biting his neck, his evil side separated from his body, forming Dark Rockman!

Tesla:
Episodes: 25, 30, 46, 47, 48, 50, 51
For her 29th birthday, Tesla receives a Synchro Chip. Since she is the leader of the evil organization Neo WWW, that could mean bad news. However, since Dark Rockman caused her empire to crumble, she joined the Cross Fusion members in their fight against evil.
Charlie:
Episodes: 41, 42, 45-48, 50, 51
When Cosmoman breaks Netto's Synchro Chip, its up to his friends to fill in his place. One of those peoples is Charlie Airster, who helps stop a truck from falling off a cliff, using Cross Fusion.
Episodes: 42, 45, 46, 48, 50, 51
Nenji, Dingo, Jasmine and Princess Pride, have their Cross Fusion debut in episode 42.
Episode: 48
Remember waaaaaaaay back in the day when Rockman and Blues used the Double Program Advance to defeat Pharaohman? Well, as a matter of fact, there
is a Triple Program Advance. When Slur obviously overpowers Rockman, Blues, and Searchman, its up to the Triple Program Advance! But will it be enough to stop her? *cough* no... *cough*
Note: This is the first time a Triple Program Advance is ever used.
Battle Chip Combinations:
Rockman:
Spread Gun+Spread Gun+Spread Gun=Hyper Burst
Blues:
Flame Sword+Aqua Sword+Elec Sword+Bamboo Sword=Elemental Sword
Searchman:
Vulcan+Vulcan+Vulcan=Mugen (Infinity) Vulcan

Episodes: 43, 46, 50, 51
Dark Miyabi must choose between living a restricted life as an assassin or being an ally with Netto. Luckily, Miyabi chooses to be on the good side, and Wily gives him his own Synchro Chip in order to Cross Fuse. ^.^

Episodes: 50, 51
Wily seems to give Synchro Chips as if it were candy, since he gives one to Barrel, so he can save the world from erasure (as you have already heard from me about 10 times). The sad thing is, we only get to see him for about 2 episodes..... :-(