Let me explain Bass's timeline. At least the way I see it, feel free to believe me or not:
Before the games:
-Cossak creates the self sufficient Navi, Bass.
-The current network becomes sentient, causing network problems all over the world.
-Bass is blamed for the network problems and is presumably deleted, but he manages to escape, and survives for years by absorbing the remains of broken viruses and navis.
Battle Network 1:
-Unknown, he does appear as a random encounter, but since it isn't a plot battle, not a lot can be said about it.
Battle Network 2:
-Angry at the idea of being copied, he invades the WWW server and deletes all of his copies.
-MegaMan and Bass fight for the first time in the WWW server.
Battle Network 3:
-Bass strikes an alliance with Dr. Wily to revive Alpha and destroy all humans.
-Bass is tricked by Wily into absorbing Alpha's guardian program which weakens him.
-Bass fights MegaMan in his weakened state but is absorbed by Alpha halfway through.
-As Alpha is being deleted, he somehow manages to escape by merging with the remains of either Gospel (I dunno how that happened, but it did), or a similar entity, but becomes fragmented as a result.
-Bass is restored to full power through a gathering of BugFrags. Having no prior memories, his only goal is to prove that he is the strongest. He fights MegaMan but is defeated. Unable to comprehend this, he disappears in search of power.
Battle Network 4:
-It's unknown when this happened, but I assume that during his search of power, he ran out of energy and turned to stone. Yeah I know, lame story.
-Bass is revived upon making contact with MegaMan's DarkSoul, but is defeated once more. He escapes, hinting that he's going to find a greater DarkPower.
Battle Network 5:
..errr I haven't completed my Bass Cross game in Double Team DS, so you'll have to forgive me for not having any data here. But I assume he's angry at MegaMan for mimicking him and tries to defeat him but fails. What I do know, is that the ChaosLord is a completely different entity that only mimicks Bass.
Battle Network 6:
-I dunno why, maybe he was tired or something, but he was sleeping in a grave, when MegaMan came by and awakened him... again. He fights and loses... Again.. And escapes... Again.
-Wanting revenge on MegaMan, he battles him again in the Network Graveyard, but loses again. He claims this to be the power of the Cybeast, and goes off to find power.
-He finds power by somehow absorbing remaining data of the Cybeast and attempts to defeat MegaMan again, he fights using all he has, and ends up being deleted at the hands of MegaMan. Seriously, this is no lie, there was the explodey deletion animation and all that never happened to Bass before except for that final moment.
Even if you view all of the secret areas and postgames as non-canon, Bass's story would end when he is absorbed by Alpha and subsequently deleted.