Best Wishes: The Final Passage (Japanese: ベストウイッシュ：ファイナルパッセージBesutōisshu: Za Fainaru Issetsu) is the second Alexis Saga movie. It was released Worldwide on July 31, 2012. The movie was set between BW162 and B2W2-001.
The movie feature Alexis, Whitlea, Blake and Team Plasma in prominent roles. Legendary Pokémon Zekrom and Reshiram also make an appearance, among several of Alexis's friends.
Alexis runs towards a cave entrance, in which she quickly lets out her Pokémon, revealing to them they will be having a new journey by themselves. Meanwhile, back at the League, the whole event is bombarded by Team Plasma and their Pokémon, tearing the league to shreds, battling everyone in sight. Elesa, Brock, Caitlin, and Falkner are quick to spring into action, helping Nurse Joy help the injured, and aiding Officer Jenny in her bid to recover what is left. A young green-haired boy and a caped man suddenly walk into the ruins, eyeing their sights on the group, turning to each other before heading to speak to them.
The next morning, Alexis appears worn out with Oshawott and Axew by her side, turning up at a café. Alexis is horrified to hear the events that happened the past night on the news, discarding her table and heading out the door. Suddenly, Alexis is stopped by two trainers; Blake, and Whitlea. The two of them are quick to warmly introduce themselves to Alexis as past friends, however, Alexis stands their, unbeknown to who they are. Puzzled, the two quickly explain to Alexis what happened at the League, and invite themselves to join Alexis. Alexis, still confused, is quick to spot some Plasma Grunts, who are heading towards the café. Blake drags the two girls to a hidden corner within the café, as the two grunts enter. They suddenly scan the café, destroying everything, it’s at an abrupt moment in which they escape, running along a jagged rocky path. Alexis demands answers from the duo, after they make camp nearby a tree. The two reveal that they are ex-Plasma members, who managed to escape from the group after Alexis destroyed their hideout. Shocked, Alexis quickly shoots down their explanation, telling them she has no recolection of any hideout or them. They are both puzzled, as they are certain of who Alexis is. Tired, the trio soon fall to sleep. While sleeping, Alexis begins to dream of a hideout, in which she’s stood in a room next to a green-haired boy, facing a man who holds two crowns. To the back of her, she see’s a room full of people, including Plasma Grunts. She is then facing two women, who are stood smiling at her. She then wakes up in a cold sweat. It’s now the morning, and Whitlea and Blake are already getting ready to go. However, Alexis reveals that she didn’t reallt have any plans, and that she didn’t know what to do next. The two reveal that she should probably escape Unova and head back home to Sinnoh. Now set on where they are going, the group are soon greeted by a group of bikers. They reveal that a public announcement revealed whoever captured Alexis would be rewarded. This is followed by a 3v3 battle between Alexis/Blake/Whitlea and the bikers. Following a smokescreen from Blake's Pignite, the three of them are able to escape. The scene then cuts to a dark cage, where Elesa, Brock, Caitlin, Falkner, and several other trainers with their Pokémon. They are soon met by a woman. She explains to them that Team Plasma mean no harm to them, and all they want is to have Alexis. She is then interrupted as a man walks in, who introduces himself as Ghetsis. He tells them to tell him where Alexis is immediately. They all reveal they have no clue, leading to Ghetsis confiscating all their Pokéballs. They all shout in disgust, but Ghetsis walks away. The woman reveals that unless Alexis turns herself in, or is turned in by someone else, Team Plasma will not go quietly. When asked why, she reveals that Alexis stole something from them and betrayed them. She also revealed that Alexis was an ex-Plasma member, and the sister to Lord N. Alexis had betrayed Team Plasma by taking a special stone used to awaken a mysterious Pokémon. She finished by revealing that noone knew where Alexis was until she was spotted in Castelia City running away from Team Galactic. When Brock asks why they tried to catch up to Alexis on such a big scale, she revealed she didn’t know, turning around and walking away.
The scene then goes back to Alexis, Whitlea and Blake, in which they are panting; Alexis begins to collapse and falls to the floor, Whitlea and Blake run towards her, before the screen goes black. Alexis is once again stuck in the hall besides N, in which she looks towards the floor, where a happy Tepig sits. She smiles at it, and then looks back at the man. He puts the crown on her hed, in which everyone claps. The scene then moves to Alexis and Tepig walking towars a room. Alexis seals the door behind her, and quickly runs towards a chest. Alexis opens the chest, revealing a glowing stone; which she puts into her pocket. The green-haired boy walks in with some Pokémon, following Alexis battling him, she runs out of the room, and is soon met by Blake and Whitlea, who ask what she’s doing. She runs past them, but is followed by an army of grunts. Alexis, still running, soon realises that her Tepig falls behind, being captured by the grunts, in a tearful goodbye, Alexis is urged to go on without it, which results in Alexis ordering the Tepig to blow up the lair with it’s flamethrower, in which it does so. Alexis then appears laying on the floor crying, before waking up aside of the road with Blake and Whitlea again. She soon unleashes the dream on them, in which they reveal that those events happened. They then reveal that the hideout was destroyed, but everyone got out alive. Team Plasma then rebuilt their empire, and there only plan was to get the stone back off Alexis. When Alexis asks about the Tepig, they reveal they don’t know. The gang then turn up at the Castelia Bay, in which they are all set to depart to Sinnoh. However, Team Plasma turn up, surrounding them. Ghetsis then appears, with Alexis’s sister, Dawn, and mother captured. Whitlea then stands by them, revealing that she was infact never not in Team Plasma. Alexis and Blake are then taken away. As they appear back at the Plasma hideout, Ghetsis reveals that he wants the stone back, but Alexis reveals she has no recollection of having a stone, in which a battle ensures between them. Alexis is then hit by Ghetsis’s Pokémon, which she falls to the floor, passing out. The dream continues, showing Alexis walking alone speaking about the events to herself. As Alexis wakes up, she remembers all of her past, before standing up facing N, and defeating his Pokémon. It’s at this moment where n brakes down – declaring he cannot harm his sister – however he couldn’t understand why Alexis stole the stone. She revealed that from what she can remember, it was Ghetsis who forced her to run away, and that N wanted the power all for himself. She went on to explain that Ghetsis wanted her to give her stone to him, but not feeling the ability to trust anyone she ran away. However due to her apparent amnesia – she never got rid of it – and believed it was just an airloom given to her by her mother. N revealed that it was Ghetsis who alarmed them of her betrayal – and that she was planning to steal one stone and destroy the other – so N could never get the power, while she did. This lead to N giving his stone to Ghetsis. However, Ghetsis appears behind them, standing against the Legendary Pokémon Reshiram, who lets out a blaze. The stone rises from Alexis’s pocket at the sight of Reshiram, beginning to glow. From that moment, Zekrom rises from the storms of the mountains, appearing at the League. At the sight of this, Ghetsis calls the sages and asks for Reshiram’s power, and at this moment, buildings rise from the ground, destroying the league’s walls around them. The group dash into the room; being sealed off from everyone else. Blake and Whitlea begin their very own battle, while the group begin to battle with the sages. N decides to use Zekrom's power – but is soon stopped as the two women walk out – with a Tepig. Alexis and Tepig share a look before they join each other. Alexis appologises to tepig – however the two women say that Tepig was informed of what happened, and that he was just happy they were reunited.
Ghetsis and N are soon haulted in battle – where Ghetsis slaps N sending him to the floor. It’s at this moment when the sages and Whitlea are defeated, before the group are arrested by the police. Alexis then runs in front of him, and declares they battle together. After a long battle – the sages are defeated – and N appears in front of Ghetsis as he prepares an attack sent by Reshiram – in which both Reshiram and Zekrom hault – before being restored to their normal selves. They then turn on Ghetsis before being stopped by N, who haults them, and tells them they can go. Ghetsis feels like he has been let off – before N banishes him. Ghetsis then calls on Whitlea – who is ordered to push a button which starts to make the ground shake. Ghetsis runs away with Whitlea, while the rest begin to panic. They are all ordered to run by N, who knows where the bomb is planted and sets to go to turn it off. Alexis runs infront of him and tells him she will go – and for them to run. N agrees, and Alexis calls on Tepig, Axew and Oshawott to come with her. They run fast, until they finally get to the bomb, where Tepig, Oshawott and Axew use their attacks to dettatch the bomb. Once the bomb is let off – they all escape the building unharmed.
Ghetsis then appears, before being caught by the police. Whitlea however, is nowhere to be seen. N departs the group with Reshiram and Zekrom. The group then reflect – before Alexis is challenged to battle the League.
In a post credit scene, Alexis is now stood on the League battle ground, in which she looks in her bag, where a stone is glowing, it stops, Alexis closes her bag, and she walks off with her Pokémon.