In "The Fall of SKUL" it is revealed that Frank and Stella were boyfriend/girlfriend 10 years ago and that Stella had dumped Frank. Later on we find out it was because of what had happened during the final assault on KORPS. Currently Frank and Stella are not back together and their relationship is a bit complicated.
Stella still cares for Frank and was nearly crying when she thought his memory was going to be wiped and she also entered the core in "The Final Endgame" to help him even though they were both likely to die. She admitted that she was sorry for what she did and kissed him but after the core was deactivated she asked if they could forget about what happened. In "Frankenstein" it is shown she still carries the picture of her and Frank in her handbag and was very upset when he nearly died. In "The Last Stand", it is revealed how well she works with Frank and when he starts to tell her something about if the mission went wrong she just kisses him then says "There. Now mind on the mission" and runs off. She also admitted to Frank that she had told the LMH that she still loved him.
Frank also still loves Stella and admitted it during one of his LMH tests. He also apologized in the core and in "Free Runner" he was about to ask her out again when some of the pupils and teachers from Saint Hearts's appeared and he chickened out. He also trusted Stella in "We Need to Talk About KORTEX" when she said she was innocent even though she had no evidence. He also said her name when he woke up after getting a shock from The Cage in "Frankenstein"
The MI High team enjoy winding Frank and Stella up about their relationship such as when Aneisha says there is more chance of Frank asking Stella out again then Tom getting a girlfriend and when the team joke about Stella working undercover at Saint Hearts saying it's so she'll be able to spend more time with Frank.