Unlike his 1st Dimension counterpart, Doofenshmirtz apparently had a perfect childhood. This childhood is never specified, other than the fact that he lost his left eye (which he now keeps in a small pouch) for unspecified reasons and had a beloved toy train called Choo-Choo. One day, he lost Choo-Choo, and it took a toll on his emotions, molding him into a malevolent villain. A maximum of five years prior to Across the 2nd Dimension, he somehow defeated Perry (whether or not it was because they were at odds with one another because Perry was a secret agent out to stop him is unclear) and transformed him into the Platyborg, which he commanded to lead an army of Norm Bots to invade The Tri-State Area, conquer it, and thrust it into a reign in which all civilians must wear Dooferalls and play Doofopoly. At some point, one of Danville's civilians, the dimension's Candace, decided that enough was enough and she founded The Resistance, an organization bent on ending his rule once and for all. He and The Resistance have been at odds ever since, paralleling the life-long feud between the 1st Dimension's Perry and Dr. Doofenshmirtz.
Doofenshmirtz meets Doofenshmirtz-1 when he slides into his office on a theme ride-like chair. At first, the two become friends, singing Brand New Best Friend, just before Phineas-1, Ferb-1, and Perry enter the office as well. Doofenshmirtz instantly recognizes Perry-1 as a secret agent, but Doofenshmirtz-1 is unconvinced, as is Phineas-1 and Ferb-1, as Perry is in his mindless pet mode. Doofenshmirtz's attempt to unmask Perry's identity by having Platyborg assault Perry fail when he appears to be unharmed. However, he displays his first sign of his more sinister personality than that Doofenshmirtz-1's by commanding Platyborg to attack Phineas-1 and Ferb-1 next, to which Perry is forced to reveal his secret identity. The trio then makes their escape, and both Doofenshmirtzs cry out, "CURSE YOU, PERRY THE PLATYPUS!"
Later, he finds out about his counterpart's incompetence when Doofenshmirtz-1 continues to fail in identifying Perry to be his nemesis after showing him a set of photos of Perry in both pet mode and secret agent mode. He then tells him of his loss of Choo-Choo, to which he finds out that Doofenshmirtz-1, ironically, had a much harsher childhood. He also decides to conquer the 1st Dimension's Tri-State Area.
Doofenshmirtz then announces to Perry via news broadcast that if he turns himself in, then Phineas-1 and Ferb-1 will continue to go by unharmed. Perry turns himself in, but Doofenshmirtz tells him that he won't keep his end of the deal, as he needs the two boys in repairing Doofenshmirtz-1's Otherdimensionator because they did so before. He later attempted to use Perry as leverage against Phineas-1 and Ferb-1, but Perry distracts him, Doofenshmirtz-1, and the Norm Bots with an image of Major Monogram having a shower and he escapes with his owners and their companions. However, the Norm Bots manage to recapture Perry, Phineas-1, Ferb-1, and Candace-1 after a brief chase in the mine-cart railroads used by the Resistance.
Doofenshmirtz soon becomes annoyed by Phineas-1's constant refusal to rebuild the Otherdimensionator, but when Doofenshmirtz-1 finds out how the two boys did it, he sentences them to be eaten by his pet Goozim, along with Doofenshmirtz-1 when he annoys him, but the five are rescued by Candace, who tosses them a remote version of the Otherdimensionator, which they use to travel several dimensions. Meanwhile, Doofenshmirtz uses the rebuilt Otherdimensionator to enter the 1st Dimension, which he invades using a vast army of Norm Bots.
However, the 1st Dimension characters, led by Phineas-1, Ferb-1, and Perry, all retaliate, destroying many Norm Bots. Phineas-1 and Perry confront Doofenshmirtz and eventually manage to defeat Platyborg and destroy a satellite dish controlling the Norm Bots, to which Doofenshmirtz angrily attempts to kill them, along with a recently-arrived Ferb-1, with a larger robotic version of himself. But before he can do so, Doofenshmirtz-1 hands him his own Choo-Choo, and Doofenshmirtz immediately changes his ways, activating the self-destruct device on all of the Norm Bots and returning to the 2nd Dimension, only to be arrested by Francis Monogram and the Firestorm Girls for his crimes against the civilians of the Tri-State Area.
Out of all of the 2nd Dimension characters, Doofenshmirtz has the most personality differentiation from his counterpart. As the ruler of the 2nd Dimension's Tri-State Area, Doofenshmirtz is actually more evil than his 1st Dimension self. Tyrannical, cunning, and intelligent, he immediately seizes any chances available to gain more power; when his 1st Dimension self comes to the 2nd Dimension, he decides that he should "give it a try" and conquer the 1st Dimension's Tri-State Area, although this was more of a way to see if said Tri-State Area was more difficult to conquer than the 2nd Dimension's.
Another notable difference between Doofenshmirtz and his 1st Dimension counterpart is the fact that he is able to recognize Perry the Platypus without his hat on, something 1st Dimension Doofenshmirtz is incapable of doing.
Doofenshmirtz is actually also willing to eliminate those that pose as some significant obstacle in his plan (or at least those that disappointed him in some way), once ordering the extermination of the 1st Dimension selves of Phineas and Ferb to expose the 1st Dimension Perry's secret identity. He then ordered the feeding of the same Phineas, Ferb, and Perry, along with the 1st Dimension selves of Candace and even Doofenshmirtz to a Goozim, Phineas and Ferb for refusing to reconstruct the Otherdimensionator, Perry for failing as leverage against Phineas and Ferb, Candace for being incidental, and Doofenshmirtz for just being plain annoying to him. However, this plan failed. He would later attempt to strike down Phineas, albeit with a baseball launcher, when he begins to stop his plans, but he was foiled by Perry. He then attempted to smash Phineas, Ferb, and Perry by crushing them with a fist from his giant robot shortly afterwards, but he was interrupted by the 1st Dimension Doofenshmirtz.
Despite him being a darker and more sinister version of the 1st Dimension Doofenshmirtz, he still has his flaws and lighter sides, like his 1st Dimension counterpart: he would burst out into monologues; he sometimes slips into a goofy personality, very briefly so; and he, in an act of irony, would also mindlessly include self-destruct devices on his Norm bots. Additionally, his good side immediately returned when Doofenshmirtz loaned over his own Choo-Choo, causing him to change his mind in taking over the 1st Dimension Tri-State Area and end his reign in the 2nd Dimension Tri-State Area.
Doofenshmirtz is possesses the same physical appearance as his 1st Dimension counterpart. However, he has a slightly different hairstyle; wears a black buttoned-up labcoat, gray pants, black boots, gray gloves, and an eyepatch with a scar running over it (exactly how he came to have the eyepatch is unknown); he doesn't slouch; and he has the ability to grow facial hair, something that the 1st Dimension Doofenshmirtz wanted to have ("Crack That Whip").
Perry, a.k.a. "The Platyborg", is Doofenshmirtz's second-in-command and Norm Bot army general, to whom he often issures commands. They may have possibly been rivals in the past while Perry had supposedly been an O.W.C.A. agent before he was captured and converted into the evil half-cyborg hybrid he is now.
When he and the 1st Dimension Doofenshmirtz meet, they initially befriend each other and team up to capture Perry, then force his owners into reconstructing the Otherdimensionator. However, when he realizes that the 1st Dimension Doofenshmirtz is incompetent at being evil and annoying, he betrays him and attempts to feed him to his pet Goozim, along with Perry, Phineas-1, Ferb-1, and Candace-1, but fails when Candace-2 reveals herself in the Goozim room and they all manage to escape.
When the 1st Dimension Doofenshmirtz hands over the toy train he'd had as a child, which, alike that of his 2nd dimension counterpart's which had been lost is called 'Choo-Choo', he has a massive change of heart and makes up with his 1st Dimension counterpart. There appears to be mutual forgiveness between the two after that, but it can't be certain.
Candace Flynn-2 and The Resistance
Candace and The Resistance are Doofenshmirtz's nemeses, who have been at odds against each other for a maximum of five years. Not much about this relationship is known, but it appears to parallel the feud between the 1st Dimension's Perry and Doofenshmirtz, and a continuation of its long-since ended counterpart of that dimension.
When his Norm Bots had managed to subdue Candace, he didn't have her turned into a cyborg, unlike Perry, and it is unknown why. However, she'd been rescued shortly thereafter, and because of that may have had been spared from such a fate.
Vanessa is Doofenshmirtz's teenage daughter. Their relationship appears to be strained, as she angrily reprimanded him for banishing a boyfriend of hers prior to the film and telling him she might not lead a social life if this keeps up, to which he makes a nonchalant reply. He also seems to be unaware of her current feelings.
Role in the series
Doofenshmirtz-2 will soon appear in the moviesode, Spongebob and friends in Phineas & Ferb: Across the 2nd Dimension, as a member of the Villain League. In it, he will manipulate Dr. Nefarious and the rest of Team nefarious into helping him destroy the Shell Louge Sqaud and Resistance Squad. Dispite being a reitca od Doofenshirts, it's interesting he's actselly in anyway villain leage material, or that leage even wants him at all. But alchourse, a cronicles episode, The Revenge of the Second Dimension, proved that Doofinsmirtz-2 still earnestly cares for the original Dr. Doofinsmirtz and wants to see if he can bring Team Nefarious-2 and their leader, the much more powerful Doctor Nefarious-2, to shape up the original Team Nefarious as an act of repentence.